I'm an idiot, that's the problem. I forgot to tighten the clamp on the engine side of the carb. I'll tighten it when I get home today and test again, hopefully that solves the issue. Just in case I still have the problem, here's my thinking on the issue:
I picked up a set of FMF
stage 1 jets (includes needle) for cheap. I've read a lot of stuff that people don't like FMF jets, or so it seems, but they were cheap. If they don't end up working out I won't be worried. I can see a lot of difference in the factory needle vs the FMF needle, but the FMF needle doesn't seem to have a part number on it, so I can't tell any specifics other than it came with the stage 1 kit.
I installed the new needle instructions say to install the clip on notch #2 and for the WR450 say to use a 140 MJ , or a 148 if the air box is modded (mine is.) Initially it was stuttering around 1/2 throttle, so I moved the clip to #3 and that's resolved. If I understand the graphs (link in the original post) of where the different carb functions come into play, >3/4 is the MJ. The issue I have is that the largest MJ the kit came with is 150, so if that isn't big enough I have to figure out where to get the right jet for the needle.
I must say just with changing the MJ/needle power down low is much improved. I always thought this bike was strong before, on a hard acceleration from stopped I'd be riding the tank just to keep the front tire close to the ground in 1st/2nd and the tire would come up a little in 3rd. Now 3rd is almost like 1st/2nd. I know the "seat of your pants" dyno isn't terribly accurate, but 3rd gear told me there was definitely an improvement.