The popping is a lean idle circuit. At 3 or so turns out, its almost the limit of adjustability of that pilot jet. If you get to about 4 turns out, on the mixture screw, and it still pops, then you need to go one up on the pilot jet and readjust the mixture screw. The pilot jet controls the idle mixture, and the mixture screw fine tunes the pilot jet.
One of two things is making your pipes run red. One, is the new pipe has thiner walls, than the stock pipe. Two, is the motor is running lean, on more than just the idle circuit.

 

My pipe glows so red it almost looks transparent and I'm not running lean.Look at your spark plug to see if its running rich or lean.

 

so if I turn the mixture screw out like 3.5+ turns it should help eliminate that problem??...I think its only out like 3 1/8 turns right now...dont see how a 3/8 adjustment would make a difference. It sputters like crazy at high rpm...runs great when choked...and seems to run better with less pop back when I hold my hand slightly over the air box.

-Mike

 

Looks like you did a good job troubleshooting the problem. It runs better when choked and holding your hand over the air intake, both will make the mixture richer.
4 turns out, from lightly seated is about the limit of adjustment, going further doesnt effect much...until it comes completely out. Sometimes, a 1/4 turn is enough. In the long run, youd be better off with a bigger pilot...because if its at the rich end of travel now, youve got none left to go, ....for instance, once it gets cold, and you need richer mixtures at idle, it wont have any more to go.
If its sputtering at higher prm, and choke makes it better, then you need to be richer in the main jet.

 

Go up a size on the main jet. Maybe 2. The jets probab;y go up 15 steps from where you are, So you certainly don't have the bigeest one. Get the main jet correct first, it's the most important.

 

Yea I know i need a bigger jet...turned the air mixture screw out 3/4 more it seems to run 10 times better. With the heavier aftermarket tires it runs faster than the stock ones did with all the mods again.

-MJE-

 

Just dump that sled and buy my 03 Z400, its for sale nice price!

 

Run with your fuel tank valve on the prime position. The vac. is starving your carb. for fuel.