It occurred to me there may be a nice way to do this with contrib so I'll put it down, but it does require different pieces playing together nicely, which doesn't always happen (:

I see two clean approaches.

Using the Field API

If you want to use the Field API to create/update/delete fields, then I still think you should use custom line item products. I'm a little surprised it doesn't have the option of displaying the form at checkout built-in. Maybe a module will be built to add that, it should be relatively simple. But in the meantime this might get you there with existing contrib:

1. Install editablefields and Commerce Views Pane.
2. Create a custom line item type for the customisable product. Add the necessary fields but don't configure them to show up on the add-to-cart form. Also ensure the line items can't be combined.
3. Create a line item view that accepts an order ID as an argument, and add the fields you'd like to edit (and give them the editable formatter). Add a filter to ensure it only displays line items of the correct bundle. You can test the view in preview by creating a new order with a few customisable products, find the order ID (eg. from the checkout page), and pass that order ID to the Views preview. It should show you a row for each customisable line item. I wouldn't try to get the Views pane working until it works in preview.
4. Add that view as a checkout pane.
5. Make a circle of salt around the server and whisper a prayer.

Creating a custom pane and storing data serialised with the order

This has the disadvantages that you can't use the Field API to set up, modify, or read the fields (so no Views). checkout_pane_example.module shows how to do this, adding a nickname and second email field and storing the data with the order.

Ugly method

I think you could probably do it with Commerce Fieldgroup Panes if you create a field collection with the fields you want, and then add it as a multi-value field to the order entity. You'd need some code to ensure only the correct number of field collections are shown (to match the number of line items that need customising). This method feels dirty and has two concrete drawbacks I can think of:

1. As you add more customisable products the order entity will get more and more fields.
2. You can't associate the customisations with a particular line item (what if I want a want one message on my red sweater, and a different one on my blue sweater - which message goes with which line item?).

It occurred to me there may be a nice way to do this with contrib so I'll put it down, but it does require different pieces playing together nicely, which doesn't always happen (:

I see twothree clean approaches.

Using the Field API and contrib

If you want to use the Field API to create/update/delete fields, then I still think you should use custom line item products. I'm a little surprised it doesn't have the option of displaying the form at checkout built-in. Maybe a module will be built to add that, it should be relatively simple. But in the meantime this might get you there with existing contrib:

1. Install editablefields and Commerce Views Pane.
2. Create a custom line item type for the customisable product. Add the necessary fields but don't configure them to show up on the add-to-cart form. Also ensure the line items can't be combined.
3. Create a line item view that accepts an order ID as an argument, and add the fields you'd like to edit (and give them the editable formatter). Add a filter to ensure it only displays line items of the correct bundle. You can test the view in preview by creating a new order with a few customisable products, find the order ID (eg. from the checkout page), and pass that order ID to the Views preview. It should show you a row for each customisable line item. I wouldn't try to get the Views pane working until it works in preview.
4. Add that view as a checkout pane.
5. Make a circle of salt around the server and whisper a prayer.

Using the Field API and combined line items (involves code)

If you'd like to have a single line item have multiple customisations, then you need to set up the fields to allow that.

1. Create a field collection with the fields you'd like.
2. Add a multi-value field collection of that type to the appropriate line item type (ensure it won't show up on the add-to-cart form).
3. Create your own checkout pane that displays the field edit form. You'd read the quantity from the line item and display just that many fields (as it's a multi-value field it'll save ok however many there are).

Creating a custom pane and storing data serialised with the order (involves code)

This has the disadvantages that you can't use the Field API to set up, modify, or read the fields (so no Views). checkout_pane_example.module shows how to do this, adding a nickname and second email field and storing the data with the order.

Ugly method

I think you could probably do it with Commerce Fieldgroup Panes if you create a field collection with the fields you want, and then add it as a multi-value field to the order entity. You'd need some code to ensure only the correct number of field collections are shown (to match the number of line items that need customising). This method feels dirty and has two concrete drawbacks I can think of:

1. As you add more customisable products the order entity will get more and more fields.
2. You can't associate the customisations with a particular line item (what if I want a want one message on my red sweater, and a different one on my blue sweater - which message goes with which line item?).

It occurred to me there may be a nice way to do this with contrib so I'll put it down, but it does require different pieces playing together nicely, which doesn't always happen (:

I see two clean approaches.

Using the Field API

If you want to use the Field API to create/update/delete fields, then I still think you should use custom line item products. I'm a little surprised it doesn't have the option of displaying the form at checkout built-in. Maybe a module will be built to add that, it should be relatively simple. But in the meantime this might get you there with existing contrib:

1. Install editablefields and Commerce Views Pane.
2. Set up the line item types appropriately. Don't configure the fields to show up on the add-to-cart form and ensure the line items can't be combined.
3. Create a line item view that accepts an order ID as an argument, and add the fields you'd like to edit (and give them the editable formatter).
4. Add that view as a checkout pane.
5. Make a circle of salt around the server and whisper a prayer.

Creating a custom pane and storing data serialised with the order

This has the disadvantages that you can't use the Field API to set up, modify, or read the fields (so no Views). checkout_pane_example.module shows how to do this, adding a nickname and second email field and storing the data with the order.

Ugly method

I think you could probably do it with Commerce Fieldgroup Panes if you create a field collection with the fields you want, and then add it as a multi-value field to the order entity. You'd need some code to ensure only the correct number of field collections are shown (to match the number of line items that need customising). This method feels dirty and has two concrete drawbacks I can think of:

1. As you add more customisable products the order entity will get more and more fields.
2. You can't associate the customisations with a particular line item (what if I want a want one message on my red sweater, and a different one on my blue sweater - which message goes with which line item?).

It occurred to me there may be a nice way to do this with contrib so I'll put it down, but it does require different pieces playing together nicely, which doesn't always happen (:

I see two clean approaches.

Using the Field API

If you want to use the Field API to create/update/delete fields, then I still think you should use custom line item products. I'm a little surprised it doesn't have the option of displaying the form at checkout built-in. Maybe a module will be built to add that, it should be relatively simple. But in the meantime this might get you there with existing contrib:

1. Install editablefields and Commerce Views Pane.
2. Create a custom line item type for the customisable product. Add the necessary fields but don't configure them to show up on the add-to-cart form. Also ensure the line items can't be combined.
3. Create a line item view that accepts an order ID as an argument, and add the fields you'd like to edit (and give them the editable formatter). Add a filter to ensure it only displays line items of the correct bundle. You can test the view in preview by creating a new order with a few customisable products, find the order ID (eg. from the checkout page), and pass that order ID to the Views preview. It should show you a row for each customisable line item. I wouldn't try to get the Views pane working until it works in preview.
4. Add that view as a checkout pane.
5. Make a circle of salt around the server and whisper a prayer.

Creating a custom pane and storing data serialised with the order

This has the disadvantages that you can't use the Field API to set up, modify, or read the fields (so no Views). checkout_pane_example.module shows how to do this, adding a nickname and second email field and storing the data with the order.

Ugly method

I think you could probably do it with Commerce Fieldgroup Panes if you create a field collection with the fields you want, and then add it as a multi-value field to the order entity. You'd need some code to ensure only the correct number of field collections are shown (to match the number of line items that need customising). This method feels dirty and has two concrete drawbacks I can think of:

1. As you add more customisable products the order entity will get more and more fields.
2. You can't associate the customisations with a particular line item (what if I want a want one message on my red sweater, and a different one on my blue sweater - which message goes with which line item?).