On a 1997 valkyrie, if i shorten the exhaust tubes will this upset the back pressure balance or anything?

There is total misconception about back pressure. The less back pressure you have on an engine the more efficient the extraction of the burnt gasses - however, if you shorten the pipe you could upset the tuning of the system which has been carefully factory calculated to clear gasses with the minimum of noise. Rather lay out some cash and buy a custom tuned exhaust for you machine.

Yes, cutting the tubes can affect performance. If you wanted to change, consider a tested exhaust system. Some of the is stuff is interrelated, and the only way to know for sure involves a dyno. A dyno is not a home tool, usually.

That being said, serious backpressure changes happen more when baffles are altered, the length of the pipe often does help the exhaust to be stable, thereby allowing new exhaust to exit the combustion chamber correctly...