I'm not trying to be a wiseass or something but may I suggest a few steps that might do the trick?
1) get new spark plugs
2) put in a full tank of higher octane fuel.
3)take it to a clear straight road and open that engine up to the redline on gears 1,2 and 3.
4)try and repeat step 3 a few times.

That engine needs some thrashing and buddy,engine rpm in relative to speed especially at the kind of speed you're talking about is about feel.You don't want to bog the engine down but at the same time you don't want to be riding on the higher rpms at the lower gears either.It's a question of balance which you might just get it with more riding time.This is,assuming your bike is in fair working order which I think it is.
just my two cents

 

Ditch the Cobra PP tuner (overpriced junk) and get something cheaper/better...I went with Dobeck's EJK after running their TFI for a few years. Great tuner & much cheaper than the Cobra, which is limited.

 

The one thing that I can't understand is how is puting a tuner on your bike going to make the bike run better when you are lugging your engine? As was said earlier, if you don't like riding around in second gear, put it in third and go faster. At that speed in second will cause you what on the tach, 2500 rpm's? The red line is much higher. I cruise all day long on the highway running between 2800 - 3200 rpm's Not one issue on my bike with 12,000 miles. Run the highest octane you can find. I'm lucky around here. I put 93 in the tank.

 

Run some BG44 through there. It will be clean as a whistle inside and I bet run smooth.

 

New plugs installed and the Cobra FI2000 Powerpro. Took it for a short ride through all gears and ranges. Redlined all the way through 3rd. Bike is running way better. No decel pop at all anymore. No dropping out in 3rd gear. Better throttle response. Engine seems to be running cooler (won't really know till tomorrow). Starts right up and idles smooth. Takes off smooth. Just has a better overall feel. I am happy for now.

Will post more after tomorrow's poker run.

 

First they sell you a stage one download....
then they tell you it's no good - you need to replace it with a tuner. Nice!!

 

Exactly!
I bought the Cobra Powerpro from another dealer other than Harley Davidson and installed it myself. Was pretty simple, took me about an hour. Things are good and I spent alot less than Harleys $1000 tuner and dyno they were pushing. Cant wait to get through my 5000 mile service so I can begin to work on my own bike.