Just replaced a leaking exhaust manifold which was making the truck run rich (ie:crappy). New manifold made a big improvement in the crappy running but the missing/stumbling in gear at low rpm is still there.

New complete tune-up with Motocraft parts, no codes.

Gonna Sea-foam it but are there some (free) easy things to do like clean IAC etc that could cause this without throwing codes?

 

Check for vacuum leaks. Check the condition of all vacuum pipes around the engine, check that the PCV valve is good and its tubing and check any vacuum canisters for rust/leaks.