I would probably cheat and use something such as F-22 or Super Hornet intakes. Maybe also steal the F-22 exhausts, give an enclosed weapons' pannier on the centreline, do something about the tail (maybe even give it a F-23 style V-tail), new front windscreen...
At that point you're basically building an entire new aircraft, though.
Here are the mods I can see someone doing realistically, in order of likelihood they'd be implemented in real life (also, more or less the reverse order you'd have to do them if you were building it..)
Paint the aircraft in 36170 instead of TPS. The F-35C is carrying the same HAVE GLASS V paint scheme as the other variants, and it has also been applied to the F-16 during the recent CCIP modernizations.
Apply "RAM tape" made from the thinnest styrene you can get your hands on over the panel lines. Don't bother rescribing, just glue narrow, super thin strips of plastic over all the panel lines using brush cement. Paint them a different color from the rest of the aircraft if you must, but the real F-35 just got color-matched RAM tape so it's no longer needed.
Reshape the worst of the minor intakes and vents on the fuselage, like the dorsal bleed air vents, by adding a triangle to the lip.
Sand the mating surface of the ventral stabilators so they won't sit perpendicular to the surface, but meet it at an angle, preferably so the tips are further outboard.
Install F135 nozzles looted from a couple of F-35s in place of the TF30 or F110 ones. Much easier to do than faff about with Raptor nozzles, also F135 engines are in the Navy inventory already.
Replace the TCS with the nose sensor from an F-35.
Fill and sand flush the intake ramps, eliminating both their functionality and the panel lines. They're not needed.
Chop off the front end of the wing glove fairing (upper intake lip/splitter plate) and extend the fairing to the forward fuselage, Flanker style.
Reshape the edges of the intakes so both the inboard and outboard edges are completely straight, and the inboard edge is forward of the outboard one by a few mm.