Wow, seems like you are missing at least ~6 adress lines for the graphics, maybe 3-4 more for the colors. This sort of damage must be pretty visible on the board, or some of the LSxx logic has gone bad on the top/bottom board.
- Do you have a multimeter and/or logic probe?
- Is this the old style, or new style board set (lots of small ic's on the top of the board = old style, 4 big smd chips)
The board is held together with four interconnectors that carry the data from the carts down to the main (bottom) board. This data then goes to the
PRO-CT0 chip. It is unlikely that this is damaged: You say you can run games perfectly in slot 2 & 4 with a known good top board..
So this brings us back to the first thing Xian pointed out, the interconnectors. Check them for bent pints, it almost seems like there is a bent pin touching at least 3-4 other pins in one of the interconnectors.
I had a similar problem with one line of graphics missing which turned out to be CN9, but the stuff you are missing is way worse.