@Ampz - I used my rotorary tool. I cut outside the edges of the revision 1 trim. And then sanded in, but to be honest I didn't really sand it down all that great. I thought since the n64 was a two layer board that sanding it wasn't as big of an issue.
@JacksonS - it looks like I'm getting the right voltages but the connection breaks and there is no more current flowing. I think this has something to do with the battery protection circuit because I can reset it by plugging in the smart charger for a second.
@pengy - I've checked it at all those places and it seems normal but it's really hard to test because the current stops flowing after a second when I turn it on. I've been eliminating things it could be. It still happens without the screen and I used a spare battery protection circuit and it still happens so I think it might either be the regulator or something with the console itself.
@Luke - I completely agree. I did that all through the making process but this happened after using it for a couple of days. It worked fine before that. It was all sealed and working and I didn't have any problems before hand.
Sorry for the long post. I'll try sanding it down and re checking all my wires and get back to you guys. if someone is free this week and willing to skype I'd appreciate it. I know school ha started so don't feel obligated at all.