Anybody ever do a build-up on a 350MPI? If so, what was done and what were the gains?

Check your PMs.

start with a new harness and a ecm,,cant program the current merc one..edit if it not a mefi ecm..some had a merc 555

What year motor and EFI system?

Get a new crank and make it a 383. If it is a mefi3 it can be reprogrammed.

JC Performance got 450 hp out of mine if I had the budget to make it a 383 it would have been over 500 hp

I've done a few of the older 350 Mag MPi's with a Mefi 3. Most were Procharged and made from 450 hp to 520 hp.
Get rid of the stock powdered metal rods and hyper-u-cracked it pistons.
There isn't much you can do with the Vortec heads as far as port work. More than likely, you will make them worse if you try to port them. It all depends on how much power you want. What kind of power are you looking for?
Eddie

Most of these engines dyno between 350 to 460 hp depending on cam/heads/exhaust in a N/A build.

Any MEFI 1-4 can be tuned.