I bought this 2005 YZ-250F last week from a racer and it runs funny when I take it up to the mountains. I am wondering if he's modified it for racing some how to make it perform better at racing that would hinder it some how at higher altitudes.

Let me explain my problem in a little more detail... I ran the bike around where I live and while it warmed up it was running a bit odd but was fine after that. When I say it runs funny/odd, what it's doing is "slipping". It's like a spark plug misfires or it "skips" or something. When I was at the mountain if I cruised with a little throttle on I would feel fluctuations in power... however, if I just opened it up on full throttle it pulled strong, no skipping at all

I don't know much about bikes but I know it has after market exhaust and I've heard it could be something to do with the jets. Anybody here know more than me that can help me?

It has many mods done to it. Altittude plays a important role in tuning. You will have to pull the carb and write down what number are the jets and make some adjustments from there. One at a time. Its time consuming but worth it in the long run.

check your spark plug too

How far up in the mountains? Going from sea level to 3-4,000 ft can make a difference in jetting.