I've heard the same thing about Polaris... breaking down more often than others. You are right that in 2006 there were two versions, SRA and IRS. For me, I like the handling of SRA on fast/flat trail ride. But if you would be on rocky/rough terrain, IRS is a better bet for you.
The asking price $4000 seems sound OK assuming EVERYTHING is working and NOTHING is broken. Make sure the knocking noise is gone or fixed. It can be the rod bearing that's going out which will cost you $2000 to fix. People not taking care of air filter, riding quad in mud hole always have some kind of engine problem.
That 650 is carbed but you should not have any running problem at around 5000'. I have a carbed 700 at 5600' and runs perfectly. They are jetted on leaner side from factory and it may run even better at little high elevation. But still the carb gets gummed up with today's poor gasoline quality if not ridden just for a few weeks. If I were you, I will get a EFI Kawi 750 (2008 and up) but will cost you more.
Most quad problems are caused by the loose NUT connecting the handle bar and the seat.