I'm wondering what the recommended oils are to allow for smooth shifting.

When purchased my '01 Rev3 had ATF fluid in it which sounded pretty normal.
A few weeks ago I swamped the bike in a creek and drained, flushed and replaced the fluid (using again, ATF). But now on my first ride out I notice the shifting is really difficult. At times I need to almost force it into gear, upshifting and downshifting.

Not sure why the big difference since I put the same type of fluid back in.
Is there a different type of fluid besides ATF that anyone recommends?

What did you flush it with?

I am near certain the manufacturers recommendation is 20w-40. 75 wt gear oil should also be OK as should 10w-40. ATF is in my opinion too thin.

ATF is designed for hydraulics, epicyclic gears and self or power activated clutches, not manual transmissions.

I'm with Dad on the ATF thing, not so much because of viscosity but the purpose is just not correct

Having said that,saying ATF is like saying motorcycle

There are many different kinds for many different characteristics, none of which describe a motorcycle transmission

Did you get all the water out? You would be very surprised how much water can be held in suspension, whoever said oil and water don't mix was wrong

I don't use ATF, I use GRO Gear Extreme 75W, but if you do, make sure it's the right type ATF, like Dextron III, some others are not suited for trial clutches.

Thanks for the suggestions. To answer a few questions. I flushed the case by draining the tainted oil while warm, refilling with ATF, running/riding for a good 15-20 mins, drained again, refilled with ATF. The guy I bought it from gave me the leftovers of his Dextron III fluids. So what I put in was exactly what he had been using.

Perhaps I'll try an "oil" in the recommended viscosity and see if that makes a difference.
Couple more questions:
Conventional or Synthetic?
Will I have clutch issues going from an ATF to an Oil? Do I need to tear into the clutch pack and rinse them or anything?

ATF shouldn't affect the shifting unless it is causing significant clutch drag. My question was aimed at finding out if you'd flushed it with something that had a "seal saver" component to it which softens seals (read deteriorates). ATF is favored by the guys who like sharp clutch action but it won't hurt the transmission or make shifting more difficult. Any good motorcycle gear oil intended for wet clutches should work fine.

When the motor is not running is there a noticable difficulty moving the shift lever?