Are you so sure you board "definitely isn't fried"? The power LED isn't an indication of whether it's fried or not, it could be completely on, and the board still fried - but it's blinking, and the power supply is making random clicking noises, and you're not getting video or audio? Sounds sketchy to me.
Also your pictures are very hard to interpret. We keep getting a lot of zoomed in pictures with wires going off the side and it's hard to see where they're connecting to. I think we have yet to get a decent picture of where you're wiring power to your board. I think I saw that you had wired what I assume is 12v to that voltage regulator on the front of the board which, someone correct me if I'm wrong because it's been a while, isn't even necessary unless you have trimmed the part of the board that's already delivering voltage to that area - which you haven't.
Now pay attention to this next part, because it is gold for noobs such as yourself.
A good way to go about a project such as this, especially since I assume this is your first time, is to take it in small steps, and test between every step. For example:
1. Remove the mobo from the n64 casing, test. Does the n64 still work?
2. Wire your battery to your pcb, 3.3v reg, etc. Verify that you are getting 7.4v from one point and 3.3v from another.
3. Wire 7.4v to 12v on the board, and 3.3.v to the the 3.3v spot, and negative to the ground. TEST. Does the n64 still work?
4. Wire your video and audio to the screen, test, does then64 still work?
5. etc, etc...
This way if something goes wrong, you know exactly what caused it. Ya feel me? I'm not saying your board is definitely busted, but if it is, this is a good way to go about things after you start over.
Just some thoughts, buddy. I wish you all the best, and I'm happy to help when I can!