I agree that your problem is most likely NOT lens related in this case.
"error99" is reported by the camera whenever there is an error that the camera can NOT diagnose. In essence it means "There is an error and I can not function, but I don't know what is causing it"
Any other error # you may recieve would have a specific identified cause.
The lens issue is indeed a rampant cause of "error99",. but the symptoms were there even in the newest 10Ds. I don't think it is related to your problem.
You could however try make sure that the contacts between lens and body are clean and tight.
I got some error 99 in the last feew months due to the shutter freezing in extreme cold weather.
I have not been able to duplicate the failure since (crossed fingers) but it could have been the cold temperature effecting the shutter itself,.. or it could even have been the cold temps causing a voltage/amperage drop in the batteries??? I did try several lenses at the time,. and like your situation,. it would shoot a few,. then error99 forcing me to "reboot"
Bottom line,. it sounds like your shutter is sticking. This can happen. First,.. recharge your battery. and if you have a second battery try that.. see if you can trace it to a battery failure.
If not,. it's off to Canon service for your 10D