It's a bit hard to follow exactly what's going on here, but ....
A sys4 board for Flash would expect to see flipper roms at IC20 and IC 17 and a game rom at IC14 -this is standard for this game. Sys4 would have had yellow flipper roms and the game rom must match as a yellow game rom. You can also use green flipper roms in a sys4 board - no jumper changes required - provided that the game rom is also the corresponding green version. The yellow and green game rom version are different, but both can be used in a sys4 board provided they are used as a set of flipper and game.
I'm not sure you are on the correct path with just replacing roms. You need a systematic approach. Begin by verifying psu volatges, as Nino suggested, on the mpu bard, then find your Leon test rom and work through the tests on that. This lets you test mpu split from driver - which makes the problem easier.
I'd also look hard at the reset and blanking sections, but in a systematic way!
