Out of interest, did you run it with one washer removed & the choke fixed? Did it make any noticeable difference? Oh and if you wanted to check the health of your coils they should measure 2.5 - 3.5ohms between primary terminals and 14 - 25ohms between secondary terminals (plug caps)

When you get the choke issue sorted you should probably stick the extra needles washer in to see what works best for your bike.

It's not related to your problem, and can really help the midrange performance on some vfr's.