just to be on the safe and certain side, take out your spring loaded timing chain tensioner...they are notorious for going bad on the ex...if you can push it in at all, it is shot....what happens is, when it goes bad, when under a load, your timing chain will start to slap because of slack in it...it will sound alot like a ping or tap...this may not be your problem, but i would just double check to make sure...

 

try checking your valves. i've heard of a couple of people getting work done on there machines and they never adjusted the vavles. you may need a heavier spring.

 

I have to say the timing to but not because of them being a problem on the EX. I have never heard of it being a problem but I personally had the timing pin break before because and it put it out of time a bit. This caused my Quad to spark knock know matter what gas I put in it. Anyway I think something may be loose now in that part considering you replaced the cam and bored the head. If you do your own work on your quad you should always take it for a good drive to seat all the parts then go back and make sure all the parts are still tight. If this is a timing problem remember this warning, if it goes out to far you can total the engine. You should really try to find out what it is because you can do alot of damage if you do have a timing problem.

Also if your wondering it was a 96 300 Honda 2x4 that I had the problem with. I was on grass with larger than stock tires reved it up and popped in 1st gear. I heard a little snap (pin). I got lucky though because I could have bent the valves if it had let go all together. My fault though.

I have a 99 honda 400 EX and have only changed the oil when needed and tightened the chain once. Man they built them to last thats all I can say.

1999 Honda 400 EX
1998 Honda Foreman 450ES

 

I hate to say it might be as easy as a spark plug. When going with a higher compression engine you can't run the same plug as stock depending on your compression ratio. Usually you have to switch to a cooler running plug. Whatever plug company you are running, go to their website and look at their charts and get the next cooler running plug than what you are running now. that should do the trick.