check on your voltage reg/rectifier
youmay want to upgrade to a r6 model- pretty easy
could save you some $$$ by not cooking your stater
much info here on the upgrade
2012gsxr750
07gsxr750 track(gone)
91gsxr1100
1989 fzr400
400/600 in the making
Change the headlight lamps for H4 units from a FZR1000 Exup (I think there was a 600 version too), you might want to use a pair of switch relays for this if you use 55/60w bulbs.
Fit a 520 Chain conversion when you change it.
Swap out the shock for an R6 shock, change the front end for a ThunderCat or FZR600R Foxeye (the later uses similar brake discs to your 3EN2) you need to change the dogbones too for +25mm ride height ones.
Consider a 17" rear wheel conversion, use the XJR400 it should drop into the swingarm
Have a check of those front disks, you can swap them for most 298mm yamaha's but make sure they have the smaller hole in the middle (not like the R6) Fazer 600 (old shape) are good because they tend to be younger.
Never heard of a reg rec burning out on these.
Don't read everything you believe
FZR400RR 3TJ Bimota SB6