I am going to pull my head to have machining done to put top hat valve seals on......... What else should I have done since the head is off

 

I'd check for the valve stem clearance and out of round of the guide, wear on the valve stem, head flatness, (stock tolerance is sufficient only for stock power level), injector sealing surface state, head to head gasket surface roughness (too smooth leads to head gasket failure).

If you intend to increase power significantly over the design HP (370), mill off intake runner and install an intake header and new injection lines, twin turbos, camshaft, work on pump, rebuild trans, install brakes, refurbish suspension.. oops, scope creep :-)