First off, even running the same size, the change from PWM to PWK (or the other way) will pose challenges, and should also change your power band a bit. Both are used in the class, and I am right now running a 36 PJ, just to throw more numbers and letters into the mix.
So, will making the change give you something that you do not currently have? That pretty much depends on your motor, more than anything else. The general rule of thumb is that the larger the venturi size, the more the horsepower. The drawback is, the power band narrows and is higher in the rpm range. Too big of a venturi can cause issues with fuel atomization at any but the highest rpm, so drivability can suffer.
More air = more fuel required, so jetting you are used to will no longer be applicable.
My attitude: Unless you are maximizing the handling portions of an autocross and zinging the corners very accurately already, a little more power in a narrower band will not improve your lap times, and may hurt. The driving is still king.
Mod? That’s rich! Currently I run a dirt bike motor, with the only exception being the RCE pipe, and deletion of the kick-start mechanism. The 36 PJ is what came with it, a 1996 motor I found brand new in 2000. Included was the ignition, which has not been altered even for timing from how Honda set it now 18 years ago. More stock than “Stock Moto”.
Easy to expect that the carbs run by the fastest guys are either Keihin PWK or PWM, possibly a Mikuni, but I have not spotted one in a while. Sizes 38 or 39. There may be a 40 or even a 41 on a PI motor or two, but I have no way of knowing that.