Motorcycle Repair: conditional power loss, sputtering, backfiring, 2001 suzuki sv650, continuity test

Question
I recently bought a 2001 Suzuki SV650. The bike has 3,500 miles on it, the last owner said the motor had been rebuilt. I have his records of the carbs being cleaned 1 month before I purchased the bike.
When riding through town, there seems to be almost not problems unless I ride for over an hour. There's plenty of power throughout the entire RPM range in all gears. Occasionally, I can accelerate very hard, and the problem will begin, but not always.  Once I ride it for awhile, or get on the freeway for about 10 minutes (65 - 75mph), it starts to sputter and backfire. At each sputter, the power kicks back in for just a second. After about 5 minutes of this, it stops sputtering/backfiring altogether, but now feels like it is running on 1 cylinder. It runs relatively smoothly, but has barely enough power to keep me at 65mph. Once I slow down for about 5 minutes(25-35 mph), or even pull over and kill the bike for about 2-3 minutes, it will work perfectly for a few more minutes, then repeat. After a long trip of no power, i pulled over and felt the exhaust, but both pipes seemed equally hot. I changed the plugs once, and for about 2 days, it ran perfectly, including on the freeway. Any advice could save me big $$, as I am about to commit it to the suzuki shop.
Thanks for your time.

Answer
Hi Jason,

I would need to perform several checks to accurately diagnose the problem(s).

From the description provided, I suspect ignition components to be defective or are becoming defective. I also suspect a problem with air-fuel mixtures and fuel delivery.

Things to check:

1) Cylinder compression followed by a leak-down test if necessary.
2) Valve clearances
3) Carburetors and fuel system for evidence of varnishing, rust, water, and other contaminants.
4) Fuel system atmospheric vents; tank, cap, and carbs.
5) Ignition coils; check windings for resistance and continuity, test with adjustable air gap arc tester.
6) Other ignition components-see service manual for procedures.

Cylinder compression and valve clearances must be with in service limits for the carbs to work properly.

Respectfully,
Mark Shively