Waspy and Wheezing Exhaust Note

You have a few joints in your exhaust piping...make sure there are no air leaks or you will get popping on the overrun.

SR

Yes it is. But that would be just on the outer tube as it looks like a stock header pipe with one tube inside another.

No, You should not have any exhaust leaks. That would cause the exhaust to sound as you describe. The hole in the bottom is suppose to be there, if it is a double wall exhaust. To check if it is, take a small wire or anything that will pass through the hole and see if there is another pipe just inside. Check for exhaust leaks at the two joints.

You may be wise to address the intake length on your bike as well.
The total length of your intake is too long,it includes the long piece of pipe that your air filter is connected to.You cannot be atomizing the fuel very well at low intake pressures(low rpm) with this set-up.
Move your carb back with the use of a 4Kb intake manifold from the YFM35fx atv so the cable is just able to be routed in back of and on top of the frame.Then attach an appropriate filter directly to the carb.

Air has a definite weight,the length of the intake track determines how long the column of air will be and a longer column of air will have a greater inertia effect than a short one.
The techical term is "ram tuning" and there is a lot to this.One rule of thumb is that the carb should always be as close to the open end as practical.Engines that are in a very high state of tune tend to have longer intake tracks and longer duration cam specs and open exhausts. Regular engines with air filers and mufflers and touring cams tend to have shorter intake tracks.
On the engine in question the intake pipe from the carb to the air filter creates a very long column of air,the valve timing and exhaust do not create a situation where this column of intake mixture gets completely drawn into the engine.The effect is that a certain amount of the intake charge will tend to "pile up" in front of the intake valve at lower RPM and cause reverse pressure and poor low speed running.
Jerry branch has written much on this subject and always worth a read..

Should the length between the crankcase and the filter be of any concern other than a slightly oily engine?

You stated the hole in the exhaust pipe at the bottom is factory, if it is a double walled pipe. I did try to stick some baling wire in hole, but it didn't go, double walled it is. However, I think I am getting some exhaust leaking out of it. Might the inner pipe be compromised somewhere else inside? What is a good cheap replacement if needed? How can I seal the leaks? And where can I get a new exhaust gasket?
I am looking at getting the chrome plated megaphone from www.mikesxs.net/mikesxs-exhaust.php?category_id=5.1 but I am not sure the current setup would work if I did.

Phew..as you can tell, I am in need of some major help..