Please confirm that I have your setup correct.  You have a 94mm Wiseco Flat-Top piston, Lancer's Stage III cam, a PWK 38 carb, a pod air filter, a stock header pipe, and some sort of Ryca muffler.  Your head is not ported.  Do I have your setup correct?  Did I miss anything?

Can you please post some pictures of your carb and air filter installation.  I need to see how your airfilter is installed.

Can you please post some pictures of your exhaust system.  I need to see how your muffler connects to your header, and what size baffle/outlet you have.  Also would be helpful if you had any manufacturer's data on the muffler.

Be careful with the #140 main jet.  It could be a bit on the lean side for the setup you are running.  A #140 is good for stock compression, but with the higher compression piston you probably should be running a #142 or #145.

To alleviate your "popping", set your idle speed at 1300 to 1400 rpm.  The higher idle speed is also better for your cam.

Where is the e-clip positioned in your slide needle?  There are five grooves in the needle.  Placing the e-clip in the top groove results in the leanest mid-range mixture.  Placing the e-clip in the bottom groove results in the richest mid-range mixture.  To help with the popping, try moving the e-clip to the next lower groove (one-groove richer).  Try the richer setting.  If raising the needle one-groove is not to your liking, simply put it back where it was.

Here's a pic of my muffler (I can't figure out how to do multiple pics in one post).

Your air filter is waaaaaaaaaay too small.  It probably flows less than a stock flat panel filter.  There is almost no surface area.  You are smothering your engine.  Post a picture of the carb and filter installed on the engine so we can see if there is a simple way to install a better filter.

PWK jets look like this.  You can get genuine Keihin jets from Jets-R-Us.  They also carry a quality line of generic main jets for the PWK.  I use the generics; they work perfect and cost half as much.  Use the correct jets.  No one can help you if you use parts that aren't intended for the application and then don't tell us.

Dave makes his own baffles for a similar muffler and it works great.  If you wanna make power, you gotta get the air in and the spent gas out.  There's no way around it.  Plug it up on either end and the results will be the same, no power.

If the rubber on the carburetor covers passages it's Not gonna run good.
The piston going down on the intake stroke is Trying to pull 652 cc of air through the filter. That would be okay on a small lawnmower. Imagine 650 cc of air being Sucked through that filter 1,800 times in a minute. That would be 3,600 rpm. The math just isn't coming to me, is thirty times a second? Feels wrong,, but it's working way too hard for a breath.

You may be able to put together a filter pipe to the carb that either has an "S" bend or a 45 degree bend to point the filter out the side of the bike.