FPRs wear out eventually, but the real point is you need to repair stuff before you mod. The busted vac lines for instance. Fix them now. Your FPR won't work right without vac feedback. A quick test is to get a mityvac with a gauge, hook it to the FPR and pump, see if the FPR will even hold a vacuum at all, say 10-15 lbs. That stutter might be unrelated, maybe the crank sensor... But again the point is fix the stuff you find.