Missing gears 2, 4 and reverse
 

Near impossible to get 2, 4 or reverse gears, 1, 3 and 5 are okay though. Have checked linkage at gear stick end and all is fine. The gear stick moves backwards, forwards and side to side okay, but just doesn't seem to want to engage. So am thinking either the shifter mechanism on top of the transmission has gone bad or worse something internal in the transmission.

You definatly need to check the linkage at transmission

Sounds like the bolt with the conical end at the linkage has slipped

UPDATE: As suspected the bolts on the short shift linkage had worked loose, not helped by the grease that had been over-applied to the rose joint. Cleaned everything up and used red thread lock on the bolts. All is good again.

A shame you didn't use the opportunity to install one of Only944.com's short shifter since you were in there already. Still, it only takes about 1/2 hour to install it and you can't imagine what a joy it is to shift afterwards.

I already have another type of short shifter kit fitted, coincidently I took the precaution of ordering the only944.com one too. Received it the other day and it is far superior in build quality than the one I have attached at the moment.