not quite sure why but the piston will never come up flush with the top of the block throughout the stroke, the highest is comes up is like 3/16 to 1/4 from the top, what gives?

 

Wrong pistons for the rods being used?

 

most pistons will be .030 give or take a little in the hole. 3/16ths is a bit excessive. just about have to be wrong piston/rod combination

 

what do you think i should do to go about solving this problem?

 

get new pistons or rods. Sounds like you have stock 400 rods and pistons for a 5.7in rod 400.

 

supercharge it?

 

I like the way soon2be thinks!

 

install the correct parts, or just laugh at it since it's a funny 400.

 

The difference in compression height (centerline of wrist pin to the top of the piston) between the piston for the 5.7" rod and the piston for the 5.565" rod is .135". If that's approximately what your seeing then you do have the wrong piston for the rods your using. Personally I would go with the 5.7" rod. You can get them for about $120 reconditioned with clearanced Milidon rod bolts from http://www.dirttrackthunder.com
Go to the Online Catalog, choose connecting rods and Make: Chevy. They are on the second page. Scroll down 'til you find the 5.7 clearanced rods.