I'm not entirely new to Subaru but I haven't don't much to an engine yet, however I am planning to rebuild my engine on my 98 Foerster limited, and I'm worried I'll botch it. Any advice?

Define rebuild. And please explain what is wrong with it currently and what your goals are. 

GD

I blew the current motor so I got one from a buddy, so I want to do head gaskets and see if I need to shave/replace heads, and make sure everything is a ok so I don't swap in a dead motor

That's not a rebuild. That's a head gasket replacement. Go ahead on and do it. Just swap the pistons for the 2000 - 2005 SOHC pistons and use the 04-07 STI head gasket. 

GD