I recently got a 1989 XLH1200.
Tatty but low mileage and apparently sound - but then within a couple of days the four speed box pretty much disintegrated. It started off with some horrible odd noises and rapidly ended up with not being able to shift / stay in gear.
I was able to diagnose the problem as a broken shifter cam - apparently the OEM are made from cream cheese. I found out about this in the fantastic book '101 Evolution HD Performance Projects'. (Well worth the £20 for anyone who wants to do any tinkering).
You can see the relevant article online at:
101 Harley-Davidson Evolution ... - Google Books
I got the replacement part from Hogparts for about £50 - I didn't feel confident about taking the gearbox apart myself so I got someone to do the labour for me - for about £200.
All in all not bad for something that I thought was going to be a disaster.
Hopefully you just have a problem with the primary and you don't have to delve into the gearbox - certainly you should eliminate easier to fix possibilities first - but as people have said the gearbox is notorious. But if it has gone pear-shaped it's not the end of the world.
Good luck
ChrisH