2006 yamaha vstar 650 had a bad vibration something popped in rear will not go into gear drive shaft steadily turning

It sounds like something mechanical in the hub of your rear wheel is broken. It will probably be quite expensive to fix. You ought to count yourself pretty lucky since when it broke a shard of gear or something could have lodged itself between the rapidly rotating final drive gears and locked the back wheel. The level of danger involved in that type of failure suggests to me that Yamaha designed the thing with preventing this from happening at the front of their minds

Remove the drain plug at the bottom of the rear hub ( have oil pan ready in place so oil doesn't drip on back tire. Remove the bolt on the side of that hub unit then replace the drain plug. Fill the hub unit with a hypoid gear oil (80w90) to the top of bolt hole. Then replace bolt. Do this every 3000 miles.

Your hub gear spline may be toast. You will have to remove the rear tire and shaft to check the splines on the drive hub. That is providing your clutch plates are not worn out.

there should be OEM and third party solutions to your problem...as far as a mod from a virago shaft drive i wouldn't call a "solution" considering what a major mod this is and the expense involved in executing it. i'll research some specs on some 535 shafts and etc.. let you know what i find...