First, I would stop water quenching. Air cooled wheel weights are hard enough for 1000fps loads. Since you have tumble lube bullets then I would use Lee Liquid Alox and tumble them (or a variant like Bens LLA or 45-45-10).
Second, stop pounding on that thing. Put the sizing die in your press and size them that way. The hammering is causing you the problems you are seeing. Whacking enlarges the bullet a bit before it goes through the small part of the die and then it expands a bit around the punch before getting sized.
(yes, Lee is a good company for making good on their products. I haven't paid for a replacement part on any of my Lee presses in several decades).
If you have an arbor press you can use it with the push through sizing die. MUCH better than a mallet.
Third, if you don't know what your bore and groove dia are, then why are you sizing the .358 bullets? You can take one of those (not water quenched) and 'pound' it through the barrel (once it is removed from the pistol). Then see how much lead is 'moved'. Do the same with the 9mm bullet for a comparison. Better is to measure the resulting bullet (especially the bore dia). You can use a vernier caliper to do so, even one of the cheap Harbor Freight ones.
Yes, you can do a lot of reloading and casting without a precise measuring tool, but, I would not be without my vernier caliper. Most of the time it is used to measure overall length of bullets so I can set my seating dies correctly.