I've done a lot of work on my carb being at high altitude. My 04 Ridgeback seems to always need some adjustments on the carb. The best info on carb adjustment is the S&S Manual for the Super G. You can get it off the S&S website, no charge. It's a pretty easy carb to adjust, jet and set up if you follow the steps. Also, the enrichener on your carb can be leaking by, causing a perpetual rich mix. Might be something worth looking into.
You said the bike starts, runs, but then after a short warm up begins to sputter. It's natural for the mixture in these engines to become rich once they warm up. It sounds to me like some jetting, adjustment and checking the enrichener may help.
As for the electrical problems, the EHC is unlikely to be bad since you just had it replaced. I've had issues with the connections to the EHC and have cleaned them, secured the connector, fixed shorts due to wire insulation wearing through. My latest was the corrosion in the connector which I cleaned and applied some conductive grease, the bike has never ran better. By the way, I still have the original EHC installed and each time I thought it was done it turned out to be something else usually simple.
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