[Spinnaker]

When I first got my 2000S it would not shift into 2nd very well and would pop out of gear on occasion. Replaced the front motor mount and the shifting got a lot better and it doesn't pop out of gear anymore, but I still have to be careful to pause slighty between shifts to let the synchros catch up before shifting. The second gear is a common problem with the 6 speed tranny and you never know how the previous owner(s) treated the tranny. Check the shifting cable adjustment and the motor mount first before looking into replacing/rebuilding the transmission. If your car has a lot of miles, the front mount is most likely shot. It will be a lot cheaper than the tranny.
I used to do the 1 - 3 shift also, to avoid the 2nd gear issues. Still have to be careful most of the time going into 2nd, but at least I can still use it.