I don't think there actually was a formal recall done on the '99 transmissions - that would've cost Vic a ton of cash, and I think their lawyers got USDOT to settle for an announced "upgrade" kit which essentially was a complete '03-'05 5 speed tranny offered at a reduced price with Vic picking up half of the labor. This offer expired in late '03 or early '04, I think - just before I bought my '99, as it turns out.
Your options are to:
1 - buy a replacement tranny kit from Victory
2 - swap in an '03-'05 Freedom engine
3 - find a defunct '03-05 Freedom engine with good tranny to cannibalize.
Personally, I'd just ride it easy and plan on swapping in a Freedom engine if/when the tranny goes out. Keep in mind that it's not a 100% certainty that it will go out - there are documented instances of original '99 trannies going over 100K miles. Also, from what I've heard, they do give warning before failing entirely - popping out of gear, false neutrals, etc. - so you'd probably notice problems before it got to the point of locking up at speed.
If it does go out, it's not necessarily a death sentence for the engine - options 1 (new tranny from Vic) or 3 (cannibalize a tranny from a later engine) would keep the existing engine.
The most common & pragmatic fix is to swap in the Freedom engine; if you go that route and buy a used engine, pay very careful attention to the motor mount on the front head - a big enough side loading (from an accident bending the front end, for example) can crack the head, which won't be noticed until firing up the engine & running it for a little while.
Mine never got to the point of tranny problems; it was sidelined for other issues, and I solved the problem by getting an engine from Rylan Vos... Power upgrade and solid tranny all at once.
'99s can be a challenge, since it was the first year and many details were changed for '00 - seat fitment, for example - so you will need to keep that in mind. Nevertheless, I still like mine a lot, and have no regrets - I think they have character and are unique enough that you won't see many of them out there.
'99 V92C with K&N, PMRT chip, Vic stage 1 slipons, and engine by Rylan Vos!