Yeah exactly how the CIA and rom injection was built/done would be good to know. I had attempted to build a CIA of an unmodified GBA VC title as a test and even that wouldn't boot. I also tried building it using ScireM's 3DS Rom builder then extracting the CXI with 3DSExplorer. After converting that to CIA it wouldn't install. (though it did install while in Gateway mode. But Gateway can't boot GBA stuff, so can't test if it worked)
Probably encryption related. 3DS roms are usually zero key encrypted for Gateway. But PastaCFW and PBT CFW do not support that method of encryption for CIA files. (Gateway does however) Installing them while in Gateway mode works. But they do crash if loaded from PastaCFW/PBT.
I'm interested to know how you built yours. Looks like the sig checks in AGB_FIRM was a lie.