So I was going through my PCBs earlier and had an idea...
Here's Viper Phase 1 running on an E-JAN PCB:
Also tested on Battle Balls for same effect, will likely work on Raiden Fighters 1 PCB also.
this is with ROMs 1-6 (all the socketed ROMs) swapped and all of the SMD ROMs remaining in place, no other trickery involved... it literally "just works".
The E-JAN graphics ROMs are still in place here which is why you see "flying blocks of crap", but the game seems to boot/play fine.
To complete the conversion:
There are 8 SMD ROMs that need to be replaced for the graphics to work, unfortunately 3 of them are a weird SOP32 form factor.
U215 is the PCM ROM, and luckily it shares all of the address and data lines with U216 which is socketed and unused by Viper Phase 1, so if we remove U215 and jump the CE pins between the two (this works out to 2 adjacent pins on the main board connector so a simple solder blob would do it) it should theoretically allow you use that socket instead of sourcing a SOP32 ROM for that location. That would fix the Audio
U322, U323, and U324 are all 32Mbit SOP44 ROMs (8-bit I think). So they could be replaced with MX29L3211 but would require a voltage regulator to supply 3.3V power. That would fix the object roms.
Finally there is the Background Tile ROMs. U415 is a 16Mbit SOP44 and U410 is an 8Mbit SOP44. I believe you can find 5V SOP44 EPROMs in these sizes, worse case you can use more of the MX29L3211s. I believe these are setup in 16-bit configuration.
The tricky part here is U416 and U49, these are again SOP32 EPROMs, U416 is 8Mbit and U49 is 4Mbit. These are pretty uncommon and I don't know of any suitable models that will work here off the top of my head. Worst case you could dead bug wire up a 27c080 and a 27c040 but that'd be super ugly, there's enough room here you could also build a small adapter PCB to run some SOP44 equivalents or something else
I already have a Viper Phase 1 cart so I don't really have much ambition to take this further but based on my test I'm pretty confident that if you can complete the conversion of Battle Bals/E-JAN or RF1 to VP1 using the above described method.