I contacted Triumph Australia today and spoke with the head service tech. He was very helpful as I described all my issues with this bike.
The fork legs and exhaust are all cosmetic and have been rectified under warranty.
The engine management system is fixed. So far so good.
As for my shifting issues as soon as I told him what the issue was he immediately said he new what the problem was and I was to take it down to my Triumph dealer right away.
I took it down to them, it appears there is some shim in between the gear lever and shifter linkage, they sometimes dry out and dont allow the pedal to reset itself or something like that.
Anyway they pulled it apart and greased the splines and this shim that looks like a flat 3/4 washer.
I took it for a ride and it appeared to work itself out. It now appears to be working.
So here's hoping its ok now.