Husqvarna YTH2148 problems.

I have a Husqvarna YTH2148 with a 21hp briggs els 656 v twin. The problem i am having is that when it is idling or running at full throttle, the mower sputters. It also spits out flames on the right hand side exhaust in the muffler. I have already rebuilt the carburetor, changed/gapped plugs, adjusted valves to .004, ran premium fuel with sea foam through it. Does anybody have any suggestions. I have also checked the timing key and it is not sheared. I dont have any vacuum leaks around the intake or carb.

Double check you have not lost the main jet from the carb when you were cleaning it.
And on that subject, exactly how did you clean it ?
Usual causes of flames out the exhaust
1) running too rich
2) exhaust valve opening too early .
3) Spark happening too late
4) on Multi cylinder engines, running too lean & missing on one pot

I completely took the carb apart and cleaned it with carb cleaner and blew it out good with compressed air. I also had to replace the small gasket inside the carb that had swollen shut and was blocking air flow. I did let the carb sit in cleaner overnight also. If it is only shooting fire out of one side, would that still be a carb issue? Wouldnt it come out of both sides?

REmove blower housing & disconnect the ground wire to each carb.
Not you will have to ground both of these to stop the engine if the fuel shut off solenoid is not working properly.
Also remember 3 or 4 minutes without the blower housing on tops then you start getting into the head overheating territory.
Problem goes away then try again with both the coils hooked up together
Problem comes back = diode between the coils diff, get a replacement sub loom.
Problem does not come back = mower wiring problem causing the magnetos to randomly ground out.

I will definitely give that a shot. It wont be until tomorrow before I can tear back into it. Thank you for the information!

And did you mean disconnect the ground wire at the bottom of both coils?

Yes,
That wire should also have another connection around the starter.
Usually it is a stand alone .
So first no wires
second the wire disconnected at the terminal near the starter,
That wire has a diode in it to stop electrical interfearence from on coil to the other.
It regularly goes bad.

Okay I just gave that a shot. I unplugged the ground wires from the coils and it is still skipping real bad during idle.

Do you think possibly a bad coil on the side that is spitting fire out? What would be the best way to check the coil?

Exactly what I have asked you to do.
We check the easy bits first and the easiest bit to check is the spark.
However you can go one better and slip an inline plug tester on the spark plug and watch it flash.
If you are having flames coming out the exhaust there is little in the module that can make the spark to occur way past tdc so the charge has not finished burning when the exhaust valve is open,
However if the diode is crook, you could be getting phantom sparks which exactly why you were instructed to check the engine with NOTHING CONNECTED TO THE COILS FIRST.
Stop trying to over think and go back to first principles.
1) flames are coming out the exhaust = gas is still burning when the exhaust valve opens.
Thus either there was too much fuel in the cylinder, rich mixtures burn slower so it is still burning when the exhaust opens
The charge started to burn too late & had not finished before the exhaust valve opened
or
The charge was right & the spark was right & the exhaust valve started opening too early.

Working on the assumption that this was not happening before you cleaned the carb the most likely suspect will be the carb
However if you are doing a "miss marple" on us and hiding 3/4 of the facts from us, this will take a whole lot longer.
You are the blok with the dud mower.
I am the bloke sitting in front of his computer with a nice cup of coffee & crossiant.

Now I can write a 25000 word step by step proceedure , but you can get a better one with pictures free.
It is called a Briggs & Stratton repair manual
So for now, we check things, starting with the most likely based upon the information given.