I had something slightly similar on my alltrac. When I cleaned out my fuel filter and ran fuel system cleaner it helped, but not sure if that is your issue. That is just what I tried and it was cheap.
You said the plugs are new, but have you pulled them to see if they still look new/properly burned? That could help in diagnosing.
It is a weird issue.
i have already run fuel cleaner in the fuel system as well as replaced the fuel filter.
the spark plugs have about 10 miles on them. granted, i have not checked them recently, but i'm sure you can imagine why.
a guy on ToyotaNation replied to my post there and suggested that i look into clutch chatter. so, i watched a few videos on youtube of different vehicles with clutch chatter and it is EXACTLY what i am experiencing.
so... i get to replace the clutch kit that has 4000 miles on it. thankfully, the Exedy OEM clutch kit is only $100. pulling the trans will be a bit annoying though. at least it will allow me to repack the throw out bearing with better grease - yay!
that is the route i am headed currently and i will report back if that does resolve the issue.