You asked, "What would you [I] do?"
Unless I really ENJOYED repeated frustration, I WOULD NOT TOUCH THE CARB 'TIL I WAS READY TO COMPLETE THE JOB.
That is, wait 'til all the add-on exhaust parts are installed, etc.
Otherwise, you must wrestle with your carburetor at least TWICE; tackle that miserable, troublesome "choke" cable connection to the carb body; drop the float bowl, etc., etc. Not to mention, removal-and-insertion of the carb into the "hoses" connecting it to the head and to the airbox; loosening/tightening/loosening the hose clamps, and so on . . .
Glutton for punishment? Do it now, and then, when you get your exhaust, do MOST of it all over again.
Also, I have LIMITED expecations for the effect of re-jetting; beyond the 22-cent mod, I think Kawasaki did a fair job, developing air/fuel mixtures for the KLR650.
The new exhaust may justify re-jetting, but . . . what are your expectations for the new exhaust?
An achievable goal, certainly!