Sorry bud, But I call bs on this! I happen to have had the opportunity to meet, ride, chat and wrench with a lot the Cat engineers and Suzuki engineers when they would come test in my area through the years, I happen to have some crank issues with my m1000 after about 1500 miles or so. So after talking with them about it they explained to me how important the clutch is on the 1000 twin because it is the only Counter balance on the motor which is needed with the bigger Top end in the 1000. They said 95% of cats 1000 crank failures were from unbalanced clutches From the factory due to the factory tolerance specs being to broad and Cat not wanting to pony up the extra dough to get them in proper Balance with each motor. Number 2 reason from Clutch failure of some kind going un noticed and really sending the clutch out of balance. That's why some people end up with 5000 miles on a 1000 and some only got 500! The un balanced clutch slowly slops out those bearings and it continually gets worse till crank failure!
They also said to NEVER EVER run the engine without a Clutch because it would cause damage to crank bearings!
So that being said im not doubting your balance skills but your test was Bs that Crank was worn out from that OUT of balanced clutch you pulled off it and Rebalanced! Then you fire up the old trashed motor with No clutch! Of course its going to shake like hell!
Try Apples to apples take your crank mod and those bearings and compare it to a New Factory Crate motor with a Properly balanced clutch and show us that Test! Suzuki knows how to build a motor! 1000 cat problems were on cats clutches! Not a bad motor!