Usually if the IMRC's are whacked it will throw a code. Mine did on the 98-
So unless the hesitation comes in around 3,300, I wouldn't suspect those.
I know what you are talking about though. My 98 Cobra did it to me once or twice over a few years. Never happened enough to troubleshoot.
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SOLD 6-17-06
'01 Silver Cobra #2709
Procharger P1SC w/10# pulley, 3 core IC, Bassani OR X, Steeda catback, 42# injectors, Lightning 80mm MAF, Tri-Ax, Fat Knob, Battery in da' trunk, JMS Tune 432rwhp / 390rwtq 12.54 @ 115 on street radials
SOLD 6-13-03
'98 Laser Red Cobra #634 of 5174
UPR Power Pipe, BBK off-road H, Flowmasters, 4.10 gears, battery relocated to da' trunk, rear seat delete, Cobra R 17x9 rims with Nitto 315's out back, shaved door locks, 13.35 @105