mostly second gear, seems like I get a good solid 'clunk' but then it's 'in between' wherever that is. What's up with that?

it's a 2000 five-speed

 

adjust your gear shifter a tad lower?

 

I can barely get my boot under it now, was actually thinking raising it a bit.

Guess I'm just hitting neutral on the way to 2nd though it feels and sounds like a solid engagement. Used to get that on my Sporty if I was a little lame on the one-two shift.

 

Can probably adjust the clutch cable some, I adjusted mine after swapping my bars and I have that "click feeling" back.

 

What he said but do a full on clutch basket and cable adjusment unless you have already done it.
That's about the only other thing other than checking the oil level.

 

I think you need to take the outer primary off and inspect the inside.

......maybe compensator on its way out or tensioner needs to be tightened???

 

How many miles is on the bike?

If you feel it hit neutral and clunks hard when it goes into gear. First a clutch adjustment like other has said, Change the transmission fluid and inspect for metal on the magnet.
Did this happen all at once or did you just get the bike?

 

Bike's got fresh fluids and clutch adjustment a month ago. Had the primary cover off as well for a general inspection (just got the bike) everything looks good inside, 20k miles on it. Compensator looked fine visually. I didn't adjust the chain tensioner, maybe that needs a check? It is a little difficult to find neutral. Never missed any shifts until this last week or so. Doesn't appear to be a chronic problem, more like something's out of adjustment. It's weird, my previous bike you knew right away when you missed the shift, didn't get that solid clunk. This one feels like it shifted, but then you're in neutral. Doesn't seem to happen when hard on the throttle, but only when putt-putting around town.

 

Have you checked the shift arm on the tranny?
They have a nasty habit of working loose. You may need to tighten the pinch bolt on the arm.