Ehhh you have some problems man. Hate to say it, but it has to happen.
Take the intake off, fix the gaskets, and do yourself a favor and get a hanes repair manual at Autozone. Shows everything, and itll be helpful to you.
Look for the right order, and right amount of torque to put on the bolts for the intake manifold. So then thats done.
Next, get a submersible fuel hose. Make sure when you put it in, it doesnt kink.
Find out what kind of MAF it is, email your tuner see if he can send you a base tune.
Another thing, did you solder spade terminals on your Ford GT pump. Did you connect the right ones? The positive and negative are marked, just hard to see.