Mechanical timing

After getting desperate in my attempt to figure out what the hell is wrong with this thing, I pulled the cam cover and found that the exhaust cam was a tooth too far forward and the intake was a tooth too far back. Do you think that could have bent a valve or anything?

You didn't say whether you have been trying to run the bike that way or just installed the cams or what... Only two teeth off I think you probably haven't but the ONLY way you can tell without removing the head and measuring the valve stems is to do a compression test. This time, pull the cam chain ALL THE WAY OUT and insert your exhaust cam with the arrow pointing right at the gasket toward the front. PULL THE CHAIN OUT SOME MORE to ensure it ain't bunched down on the bottom some... NOW count starting at the link above the arrow (it will be #1 link) over 28 links and set the intake cam inside the chain where the 28 arrow points up at the 28th link. You might even want to take a marker and mark this link so that while you fumble with the intake cam, you won't lose the 28th link placement.

You should have your plugs out... Put the cam caps on and then the center cam idler. Leave off the cam chain tensioner for now. Use a 17mm socket on a ratchet and turn the engine over REAL EASy at least twice and see if the link count and position remain correct. If they didn't your cam chain was bunched. Pull the cams and start over. If it is OK, put your tensioner in place and roll the engine over in both direcitons a bit to see if the chain bunches at the idler assembly with the tensioner installed... if it does, the chain is shot. Then put the valve cover back on.

It was ran quite a bit with the teeth off as I had no idea that my ex-father-inlaw had screwed with the top while it was in basement. So, I have been unravelling the mystery as to why it runs like crap. I set the cams to where they should be per the manual and it runs better, but still crappy. I will be buying a compression tester today or tomarrow to rule the valves out.

Once you have everything together and have verified the cam timing is correct, if it runs poorly, a valve may be bent. Get a compression tester at any autoparts store. I like the kind that you press fit into a plug hole. Remove your plugs and kick the kicker or hit the starter. It may take a couple revolutions of the engine to get the max reading. Zero when you change cylinder. Hold the throttle open when checking or your values will be low and if you can warm the bike, they will also be a bit more accurate. In this case, if a valve is bent, it won't make much difference if the bike is warm or not as the valve won't seat and your compression will be down quite a bit; probably on all cylinders. If this is the case, you can rule out worn rings by putting a teaspoon of oil down each plug hole, in turn and checking as bad rings will show the compression shooting up when the oil is poured down. ONLY do one cylinder at a time because if you dump oil down all of the plug holes at once, it will blow up in the air and make a mess. I DO know that for sure bwhahaha Bent valves ain't that big a deal except for the expense of the new head gasket and valves. Honestly, you can use the opportunity to lap the valve seats and install new seals and check the guides. If you get that far, be sure to measure stem length as your new valve stems might be too long and need to be ground to spec.

ok, all i know right now is that has been bored over and that the PO put larger pistons in. Whether they were high compression or not I don't know. But all the cylinders had compression around 170psi.

The book says 130-160psi. What kinds of numbers do you get from the high compression big bore kits like the Wisco?