Occasional stumbling with no power

Hey all, picked up my Canadian market 98 2 door 5 speed from Vermont about two weeks ago. For the first 10 miles of the 300 miles trip the car was stumbling and jerking , with power maybe 1 out of 5 seconds. Got to a gas station threw some ISOheet in the tank and didn't have a problem again for the rest of the trip. Till I got back to CT. I only assume there is water in the tank as prior to my purchase the car sat for years and was "flooded" by Sandy.
Now the car will do the stumbling thing for about 5 mins at a time, always within the same two 1/4 mile stretches about 10 miles apart ( and a couple of random times elsewhere but not for as long, just a quick misfire and then have power again)
Has happened like clcokwork. The stumbling forces me to pull over and wait for my rpms to stabilize (jerk from 200-1000 rpms over and over again).
I've redone the main grounds, and thrown probably 15 cans of isoheet in five 1/2 tanks. This is seriously starting to bug me as I now fear taking the highway and have this problem occur., which sucks since highway is why I bought this jeep.

Have you checked the spark plugs, wires, cap, and rotor? Are you using a ethanol blend fuel? All of this contributed to my xj doing similar things. Also try resetting the ecm.
Disconnect the positive battery cable, ground it on the alternator for 30+ seconds.
Reconnect cable. Get in jeep, turn key to on but don't start, turn lights on, turn lights off, now start.

Also check for any cracks in the exhaust manifold. Those will allow air into the exhaust causing the 02 sensors to read lean and fatten up the fuel to a over rich and hard to ignite AF ratio.