Copied right out of a mail from ben:
As for IPS patching.
You take your LSDJ ROM, IPS patch the SRAM MOD IPS file
Then run it through the builder program which generates an 8mb file
Then compile using the compiler with the LSDJ fix in it.
I have a new IPS patch too for the newer USB linker. I'll find it and send it to you
Which verifies what i said and answers your latest question about which IPS patch to apply.
Another mail:
If you could get a screenshot and how u triggered the bug that would be cool. There is a guide on Ninstrument.com how to compile LSDJ. Little things like NOT ticking SRAM etc...
Ok, i did never find the mentioned guide and ben did never get around sending it to me. But maybe try out the part with not checking the Save option when adding LSDJ? Who knows. Otherwise i have no further info. Hope you'll get it to work and write the guide about it!
Maybe also try emailing Ben again.
Someone should write newer software that does the same process but easier for the user. Preferably also in Python or Javascript so anyone could use it easily on any system etc. But i think only Ben would be able to do so as it's his carts and only he knows the internals?