I've been driving an early 99 for over a decade now, and with 350,000 miles on her she still runs like a top and gets 18-20 and better if I'm nice to her. She's a 6 spd like yours, 4x4, SWB, CC.
Since you've already got exhaust covered, my suggestion would be an AFE intake, and a good chip along with gauges. Get a LUK when your clutch goes, and enjoy the truck.
I swapped my factory muffler and did exactly what I suggested above to mine. The early 99 turbo is dandy in my book. Does what lots of folks are trying to get their later model stock turbos to do, just as it came from Ford.
I've pulled lots of stock trailers, and crawled through lots of pasture in those 350,000 miles, and have put in one clutch (at 200k), brakes, batteries, a couple of water pumps and alternators, and upper/lower ball joints when I did the clutch at 200k.
She has no blow by, won't use a drop of oil, will freeze you out in 110* Texas heat, and has been the best truck I've ever had - bar none.
Enjoy your new truck!
99 F250 XLT CC, SWB, 7.3, 4x4, 6spd, ISSPro Gauges, old 75 horse TS Performance chip, AFE stage 2, LUK, BTM. 330,000+ and going strong...
2000 E350, 7.3, Auto, XLT, Bone stock (at the moment) 90K
2001 F250 Lariat, 7.3, Auto, Bone stock, 83K, (April 2001 build date - truck and tranny - so no mech. diode, Chip/gauges/intake/exhaust to come)
2002 Excursion Ltd., 100K, DiPricol Gauges, DP Tuner (high idle, 60 tow, 80 economy, 120 race), Ford AIS.
Pretty big 7.3 fan...