99 Dakota won't link to scanner

[Travsaturn]

I have a 99 Dakota ext cab 4x4 with a 3.9, it while at highway speed 55+ generally flutters in the RPM area mostly while cruise is set. Say @ 65 tach is at 2200 it flutters to 2400 to 2500 then resumes 2200. My first thought was the tranny but further looking, a transmission service, and other educated opinion "a freind who has been a master transmission builder for some time" and searching leaves me stumped I have been chasing this gremlin for about 2 months, only good sign is I purchased a graphing scanner but it will not link to my truck, it will to all others I have connected it to but not myown, it will pull codes but does give a debug error prior to the code list but unable to give live data. And yes other Dakotas are involved in my other testing.
I have been told possible computer but I am currently unaware of the exact results this could have like I said I am able to pull the codes just no live data.

I do know the rise in the rpm is related to an engine misfire, just offering as much info for the most informed response.

I am going to be starting to check the grounds and also the crank sensor but am hoping to hear some good pointers prior to the crank sensor since its a B*TCH to remove being under the egr tube right against the firewall.

More info I have done a tuneup with no result new cap, rotor, wires, plugs.

I have checked most common issues and also alot of not so common...
10/29/08
I checked cleaned and retightened grounds, checked coil has blue spark, distributor is clean and tight no play in it.
Also unplugged the tps and map sensors while the truck was running, engine dropped RPM but continued to run after with almost no effect.

Also reset computer by unhooking the battery and turning the key to completely deaden the system for a couple minutes, after which the scanner linked to the EBOD live data side but on starting the truck lost the signal and have not been able to regain it again even after repeating the same steps.