need advice on what to do with old engine (rebuild?)

I recently put in a Fordstrokers 363 in my car. My old 5.0 was from Ford Racing; one of their XB3 packages, GT-40 internals, 9.0 compression, X-11 heads, B - Cam. It was ran with a supercharger for a number of years. I suspected that there was something wrong with it, something just wasn't right. Plus, I recently bought my son (16) a 90 Mustang GT (120K miles) and figured I could transfer my engine to his car once it was back in good condition.

When I drained the radiator (aluminum, 4 months old) from the old engine I had a bunch of metal flakes on the magnetic drain plug and the fluid seemed to have oil streaks in it. I kept the Oil filter and have yet to cut the top off to see if anything is inside. I know I need to tear down the engine, but other than something obviously broken or gouged, what I should look for? What can be done to either freshen it up or is required to rebuild this engine? I wouldn't be opposed to going with a stroker if I can't reuse what I have already. What would need to be done to the block and heads?

Thanks for helping the ignorant!
 
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Break it down to a shortblock and take it to a local engine builder.
The parts are probably all good, likely it needs to be honed, new bearings and new rings.

I'm also pretty sure gt40 crate engines were just stock shortblocks with gt40 heads.
 
Break it down to a shortblock and take it to a local engine builder.
The parts are probably all good, likely it needs to be honed, new bearings and new rings.

I'm also pretty sure gt40 crate engines were just stock shortblocks with gt40 heads.
They were, i had one of the crate gt40 motors in my old 89 f150, B cam, aluminum heads, similar intake to a cobra but also looked like 460 intake. But shortblock was a stock 302
 
understood, but if I were to use different pistons to raise the compression (still with pump gas) while using the same heads, I should end up with a little more power, correct? I'd probably want to change out the CAM also. I don't think the rebuild will see boost at all.
 
got the lower intake and the heads off. There was some oil in the middle of the lower intake gasket, thought that was kinda strange but it seemed to be coming up the bolt from the valley.

Didn't see any breaks in the head gaskets. Why are the front water water holes blocked by the gasket?

Cylinders still show cross hatch. About 3/4 inch from the top it has a few vertical scratches on each cylinder. Piston tops seem to be covered in carbon (dark color). Same with the valves but a lighter color.

Still need to drop the oil pan and see whats underneath once I drain all the fluid.

any thoughts?