Maybe I have missed something but why not simply re-install a center resonator, even something aftermarket, e.g., Magnaflow? Even a dimpled pipe or a pipe with bends tends to add back pressure.
If you are truly concerned with the absence of back pressure, it would be easy enough to test by simply (temporarily) restricting the end of the tail pipe with an appropriately sized can. With respect, if your engine is stock or close to it, and you are not employing long tube headers and/or an aftermarket cam, or fuel injection with an aftermarket chip, I doubt the lack of back pressure is the cause of a squirrely or rough idle.
Generally, two-cycle engines benefit from back pressure and expansion chambers. Conversely, reduced back pressure is desirable in a four-cycle engine. But for the noise usually associated with an unmuffled exhaust, we probably wouldn't need them. If the exhaust ducting is too large, it can adversely affect performance, by permitting a reduction in exhaust gas velocity. Adding restrictions to exhaust tubing may abate sound but it is rarely a performance fix.
Long distance diagnoses have never been my forté, and since I am unfamiliar with your mechanicals, sight unseen, I would only suggest revisiting some of the basics, including plugs (NGK BP5ES) gap, ignition timing and valve lash. Any or all of those "adjustables" can provoke a poor idle. Since I am ignorant regarding your mode of fuel delivery, to the extent idle mixture is adjustable, consider doing so. Again, if your engine has been significantly modified, all bets are off and please disregard the above suggestions.
hth
