Re: '99 Mechanical part of the fixup
The '99s still had OHV. Replacing the intake gaskets aren't difficult, just get a manual and take your time. You'll need a torque wrench too.
If you label all the elec connections and vac connections as you disconnect them, it'll make reassembly a snap.
As for the studder, when was the last time you changed out the fuel filter?
2000 XLT 4WD 4.0L OHV, 5 spd, Alabama Cylinder heads, Delta Cams Valve Train and Pushrods, JBA Headers, KKM Cone Air Cleaner, BBK Throttle body, Dynomax Cat-Back exhaust, Summit Racing drilled front rotors w/ EBC pads, Cobra rear disk brake conversion w/ Hawk pads, 8.8" 4.10 Traction-Lok