ddb171

Looking at the parts diagrams it is a 1996-99 Kodiak 400. I'm going by the front fender and guard. I don't know why it would have the Big Bear decals on it though. 

I have replaced 2 fuel pumps on Rincons that had very similar symptoms as you have. If you have access to a fuel pressure gauge then that's where I would start. If I remember correctly, there is an internal fuel filter that is mounted in the fuel pump housing located just above the pump that is not replaceable or shown in the parts diagram along with the one that is on the bottom of the pump that is replaceable. These are worth checking out also.

You need to get the compression reading and go from there. It could be a valve stuck open a bit and not closing all the way or something worse (hope not).  You say it rolls over good so I assume you mean it cranks fast which sounds like low compression for what ever reason.

Reread your post and see you have it fixed. What was it? Do you still need a CDI? Your post sounds like yours is working. The Beartrackers used 4XE-85540-00-00  from  01"-04" and I don't see any other number from Yamaha. Are you using OEM CDIs? 

They are known for having the intake rubber crack loose from the aluminum intake that bolts to the head. Your symptoms sound like that could very well be your problem. I have a hard time believing that you would have received that many bad CDI units.

I would go with spark plugs of all flavors, air and oil filters, wheel and axle bearings, CV boots, U-joints (Polaris), Multiple oils of all flavors. This is what I've found in my shop to be common items. I thought when i started out that when I found the common items that I'd start stocking them but it seems that when it comes to parts, I work on too many brands to be able to stock the correct items. The majority of what I work on are Hondas just because they are so darn popular in my area. Yamahas are second with lots of them out there too and Polaris 3rd because they are unreliable (my opinion only).  I'm in northern Ohio. It would be a good idea to test the waters for awhile and see what needs you have. Good luck!

Can you turn the axle when you're trying to pull it off? If not then your shoes might be wedging inside the brake hub not allowing you to pull it off. Also what Frank said, plus add some penetrating fluid. 

Make sure your brakes are all the way released too. If they are on just a little you'll never get the hub off. Been there done that.

One thing I forgot to mention, make sure your using fresh gas. If you are wondering at all if it's good, drain it and start over with fresh. Today's junk gas causes all sorts of problems.

I always have to tell my self to use the K.I.S.S. (keep it simple stupid) method when looking at problems for the first time. Check your air filter and make sure it's clean and in good shape : no mouse nests, holes or clogged with dirt. If that's all good turn your pilot screw all the way in and LIGHTLY seat it, then turn it out 2 turns. If it still runs rich turn it in 1/4 turn at a time until hopefully it smooths out. Give that a try.