My last 7.3 was pretty well done. Was a 2002 with a 6 speed so no transmission worries.
Ford AIS intake - may be stock on the big stuff, if not, its the best intake for the 7.3s. Everything else is a compromise in either filtering or flow.
Intercooler - if you dont have one, get one. You can get kits or retrofit later stuff
Intercooler boots - make sure they are tight and dont leak. Can do an air intake leak test and address them.
Up-Pipes and down pipes - Get the International up-pipes from the manifold to the turbo and then a 4" downpipe and 4 or 5" exhaust
Wicked Wheel compressor wheel upgrade - Nice lil mod, makes the turbo perform better at higher boost
EGT gauge - need to keep tabs on everything. I had an Edge CTS monitor and that was pretty slick.
Programming - 6 position flip-chips are the best, they are all about the same at this point, not a whole lot of innovation on the 7.3s. Pick one from the company that offers you the best service. I had a TS 6 position chip and it was fine.
High Pressure Oil Pump - HPOP - Eventually you will run out of oil for the injectors so you will need an HPOP uprade. Monitor the injection oil pressure with your Edge CTS and make sure it stays consistent. If it falls off at full load, then your HPOP is weak and you are not getting full fuel delivery.
Oil line upgrade - The oil lines in the HPOP system dead-head in the stock configuration. A looped oil line system ensures constant HPOP pressure. If you upgrade to a Diesel Site Adrenaline pump, this is part of the pump upgrade. I cant speak highly enough of the Diesel Site.
Fuel Line upgrade - Just like the oil lines, the fuel galleys are deadheadded. By adding a return regulator you can keep fuel pressure consistent at all the cylinders.
Injectors - Get a nice set of injectors in that 200-250cc range and get your programmer reflashed to reflect your new injectors and HPOP
Keep in mind the 2002 and up engines used powdered metal connecting rods that love to return to their original powdered state around 350-400HP, so dont go nutso if this is a later 7.3 and you need reliability. I had my 2002 about as spun up as is practical for something that just goes back and forth to church and the liquor store, never had problems other than an HPOP failure, fortunately that company is out of business now and the owner is in jail for being a POS. (Dyno Proven Diesel - you suck)