That'* pretty much exactly how mine is, the car runs great and the shifts are fine as long as you're accelerating, which isn't doing wonders for my gas mileage and makes long drives unpleasant.

When the torque converter locks up, it greatly amplifies any little variations in speed. So, just because that is when the problem shows up does not necessarily point to that as a cause. Any misfire due to plugs, wires, injectors, etc., will show up then, and not necessarily at other times.

Another cause found mainly in the 2000+ is voltage variations caused by poor connections, with the weakest link being the grounding strap pointed out above. If you haven't yet...try cleaning that up.

I did clean that one up with a wire brush and sanded the paint off where it bolts in under the seat and then put some dielectric grease on the threads and got nothing. I'm about to swap plugs out again because it'* cheap and easy enough to do to see if perhaps i just have a bad plug. and if not that i'll go over all the connections again.

OK, I lose track of who has done what. Other points are the positive connections under the seat and under the hood, and the 3 grounding bolts for the under hood fuse box. Also, checking coils, both hot and cold. You may have done these already - but it may help others who have not.

No problem, thanks for all the input. Hope to spend a good chunk of my weekend on getting to the bottom of this. So if the ground point under the seat was a culprit would you necessarily see a voltage drop at the time of the misfire?

When I cleaned it up on the car that had that problem, it was done on a whim and I had never thought before that to check the voltage level. The best answer I can come up with for it won't necessarily be very helpful, and that is...maybe.

Once the car is up and running, most of the power will come from the alternator. The battery'* job at that point (other than making up any difference at low engine speeds) is to act like a big filter to remove any voltage spikes and variations. My theory is that it is the spikes and other noises that can't be as effectively filtered out that creates the problem. Those may, or may not show up on a meter, but should on an oscilloscope. (More than you wanted to know? )

oh yea ill just break out my oscilloscope ... yea just a bit. Can never have too much information though.

I went over all the electrical connection and if they had paint between them and the body i dremeled it clean with the sanding attachment, and then i wire wheeled the connections to the battery, fuse boxes, and alternator as well as a ground that is kind of hidden under some ac lines towards the passenger fenderwell. With great hope i started things up and went on a test run, no noticeable improvement, maybe slightly greater throttle response but still the pesky cruising to accelerating shudder and hesitation.

I had today off and was left to my own devices so i detailed my underhood area and switched out to my old TPS sensor from the one that i got from a TB that i bought from Boosty since it hadn't remedied my problem. Interesting tidbit is that i had previously heard that removing the drivers side headlight didn't benefit the Bonneville the way it does on a GP when it comes to getting a colder aircharge. I guess thats only with the stock airbox, or air boxes where the filter is still under the hood because i went for a run and was seeing perfect ambient temperatures on the aeroforce for the 1.5 mile trip i went on. Thats not to hard to believe seeing as with the headlight out i could pull the filter up so half of it was visible through the hole where the light should be.

FINALLY
I had been waiting around to change my fuel filter because i tend to procrastinate and am a little nervous to get under the car even with it on jack stands rated to 4 tons a piece. Changed out the filter and then went to see room 1408 with my girlfriend. Verdict: car starts MUCH easier and sounds generally healthier when running. No more faint click/sputtering sound when going into boost, and there is still a very slight hesitation when getting on it from a cruising speed but nothing even close to before. The filter only had 62,000 miles on it but when we got back from the movie it had dried up for the most part so i tried to blow through it from the inlet side and i could hardly blow through it compared to the new one, it'* hard to believe any fuel could flow through that. I'm really glad i didn't drop to the 3.4" pulley before resolving this because i would have hated to see the result of a significant increase in boost with a fueling issue. I'm not sure but i think that would have resulted in a BOOM. I tried to launch the car from a stoplight on slightly damp pavement and the difference in power is incredible, Maybe it'* all in my head but i feel like i could hardly get traction on the damp pavement.

If anyone else is having this still check your fuel filter/pressure as well as the grounds that Archon has been telling everyone about. They weren't necessarily the issue on my car but others have had their problem resolved by cleaning them up. Mine really felt like a torque converter too but i am now convinced that it is not.

3.4", ported blower and perhaps rockers after winter here i come.