Motorcycle Repair: TRX500FA transmition, 2 quarts, horrible noise

Question
I have a 2002 Honda Rubicon,I took it to the shop to have a needle and seat put in the carb and told them to change the oil too. When I finally got it back I went for a spin and all of a sudden the trans. began to slip and grind.
Upon further inspection I found that they had only put 3qts of oil in,it calls for 5.2 I filled it to the proper level and rode it 50 miles or so. Now the trans has started makeing horrible noise (squeeling&grinding) and has even jumped out of gear once. I have tried adjusting the linkage and got it to stop screaming in neutral but in gear under load it still makes noises that will make you cringe. Is it most likely toast? Do you suppose its a direct result of running it low on oil? Anything I am overlooking?  

Answer
Being 2.2 quarts down is enough to cause trouble if you rode the machine long enough. I would take it back to them and ask them to find out what is wrong. Are they aware that the level was down so much? Had you experienced any trouble like this with it before? How long did you ride it with low oil and how hard? Is it an official Honda dealer or mom and pop shop? Sorry to hear about your trouble. What part of the country are you in?