Is there a thread on shaving the bay anywhere? Do I just weld shut the holes and bondo over? I'm a bit confused. I searched and found nothing so thanks guys!!!!

I think it's in the paint and body section. Yes you are correct though. Use a wire wheel to get the area to bare metal. Weld the hole shut and grind down the weld. If you do a good job then you can skip the bondo and just use icing on the area. Sand down and re apply if 1st coat didn't do it "usually takes 2-3 since icing is so thin". Hit it up with some primer out of a spray can to see imperfections and fix if needed. Repeat repeat cuss drink cuss and drink more repeat repeat

^^ yup what he said.

hoe do most people smooth out the seams in the engine bay ? is it a case of building up some weld along the seams and grinding down till smooth then a skim of filler ?