Kornfused RMX

What is you elevation.
from the sounds of it it sounds like the bike ran ok until you changed the gas/oil mixture. when you go from a 32:1 mixture to a 40:1 you are actually making the bike run richer. Sounds backwards right? well the way it works is, that your carb always allows the same amount of fuel into the intake (unless you change the jet size) and so when you mix your gas and oil at a certain ratio (say 32:1) that means you have 32 portion of gasoline and 1 portion of oil that is in that set amount of fuel charge going into the intake. so when you lean out you premix gas/oil (to say 40:1) you actually are makeing the fuel charge richer. (32:1 had 32 parts gasoline compared to now 40 parts in 40:1 mixture) I know confusing, but hopefully you can understand what I am saying.

Now for the short answer.
The bike is running rich and causing it to burble. lean it out. you altitude makes a diffrence.
if you have blubbering at low end end move the clip up a notch and maybe mess with the main (go down a step or two i.e. 185, 182

Switch back to 32:1 and try it. Then you will know for sure if changing the gas/oil ratio is what caused the problem.

the new top end can make your jetting change because it combusting the fuel differently then when the piston was worn a little. Every time I have redone a top end on my RM's jetting almost always needed to be redone. Sounds like it is semi rich on the top end. I doubt it is because you went to a 40:1 mix, thats what i run and I have ran 32:1 as well and there shouldnt be that big of a difference. Check fmfracing.com for jetting specs. Although they use a 50/50 mix of race gas and regular their specs always seemed to work for me when i ran 93 octane. Good Luck and let us know how it turns out.