The only person I know who has successfully done this is Motorollin over at A.org and Toni Wilen here.
You need to use the tools created by the excellent Doobrey, ROMSplit and Remus
Start with a regular A1200 KS3.1 v40.68 ROM (assuming you want to make A1200 KS3.9) which you split into separate components.
Then you combine them back into a ROM but replacing any files you like with the ones from romupdates in OS3.9/BB2 (or elsewhere).
If you want to go beyond 512Kbytes (i.e. use 2x27C400's for 1Mbyte) I think you will need to use a new EXEC and perhaps some patches.
Discuss it with Doobrey he's usually in a talkative mood.
Make a really cool guide when you're done
P.S. Your ROM's should work in WinUAE for you to test before burning...