you have mentioned how it runs at idle. but what about the other RPM ranges? i agree with Doctorturbo if its acting like that at idle adjust the fuel screw, only turn the screw 1/4 at a time, till you get it right on.

 

When you check the valve timing do it when the engine is cold.

 

It seems to run fine at all RPM ranges. So as suggested I'll adjust the fuel mixture to richen it a bit. My question how do I richen the mixture.

Thanks for the help, it is appreciated.

 

Google Image Result for http://www.dansmc.com/carb_plug1.jpg

Try this link. It's not a really good one and one that I wanted but give it a try.

Too make a long story short. You will have two screws on your carb. 1 is an idle screw and does just that; changes the idle RPM.

The other is the air fuel screw. It also does just that. Take the air fuel screw out a 1/4 to a 1/2 a turn and see what it does.

 

I called in a favor and a friend on mine came over to give me a hand. We re-adjusted the valves, to spec as some were a little too tight, while others too loose. The quad will now idle fine, and no more backfiring through the carb. But, it would not rev cleanly, and was backfiring through the exhaust. I also pulled the plug and it was really black. So I now know its running a little rich, and more adjustment was needed. I rotated the carb so I could access the pilot screw. I counted the turns in to see where it was set (2 and 1/2). I tried it at 2 turns out, it was better but not perfect.... we're so close. I think another 1/4 turn in and we got it. I'll make the adjustment and will try it again.

 

This engine should run exactly as it did before teardown or better.
Switching to a Wiseco piston does not require carb tuning.
Nor do valves go suddenly out of adjustment with the head sitting on a shelf during a rebuild.

I would check your timing ONE more time because I feel it's going to be something made from mechanical error during the rebuild process. Could even be a leaking head gasket that isn't torqued properly.
If the timing does end up being off, be sure to readjust those valves again before cranking it or you will definitely have some big problems.

I've rebuilt hundreds of engines and the only ones that never ran at least as good as they did before the rebuild ALWAYS ended up being some stupid little thing that I somehow overlooked.

There just isn't any logical reason for your 400EX to run badly just because you had it down for a rebuild. Something is not right and it's not going to be a carb issue.
It's only running a little better after tinkering with the carb because it's compensating for something else that is off.

 

The biggest problem I had was with the valves. I had the valves rebuilt, new seals etc. When I re-installed the head I made no adjustments, and the bike would not start as the valves were way tooooo tight. So I believe the majority of my issues were valve related. I had to have the valves rebuilt as well as replace the piston and rings, as the bike smoked like a 2-stroke. The piston and valves were original, and worn....

 

The backfiring was still occurring... GRRR.. So I stepped back, and started to review a few things. I was going to disassemble to recheck the timing... again... when I noticed the smell of gas... hmmm… When I took the carb of, I looked at the bottom of the carb intake boot. It was wet... closer inspection shows a crack.... Me thinks I've found the problem.... The gas I smelled was coming from the crack in the intake boot, and the noise I've been hearing (The best way I could describe it ) was air escaping through the crack... killing the engine

I was ordering the boot on-line when I noticed something strange.... The new one I ordered bolts to the spacer on the head, while mine simply slides onto the spacer. I did not like the way the intake was set up as it wasn’t very secure. There must have been a design change, and they corrected the intake.

I’ll have the part in a few days, and I post the results.

 

New parts arrived.... I put the new intake on, and made some final adjustments to the carb... I can finally say, the rebuild is complete!!!

The problem was in the intake boot leaking air.. Also now that I've increased the compression (both with a higher compression piston, and new piston and rings), I had to make some tweaks to the carb. The pilot screw is now at 1 1/4 turns out (stock is 2 and 1/4).

The bike starts easily, idles well and revs out as expected.

Thanks for everyone's help.

 

Of all the posts and it was a cracked intake boot...WoW.lol.
I'm glad you got it figured out!