If you have a ISC valve, check that the clutch switch is working. The bike will tend to die at stop signs if it isn't working. Also you can check the GPS with an ohmmeter to see what the resistances are in the various gears (the resistances are listed here somewhere, I don't have them in front of me). Check that the electrical contacts on the leads to the GPS are OK. Finally, get a real dealer mode switch. You lose any codes if you shut the bike off to fiddle around with a paper clip. There are posts here showing disassembled GPS's but you're probably better off buying another if it's faulty.
P.S. I checked my notes, which say that the resistance between the P and B/W leads is approximately:
1st - 370 Ω
2nd - 860 Ω
3rd - 1,500 Ω
4th - 2,800 Ω
5th - 6,100 Ω
6th - 17,000 Ω
The resistance between the Bl and B/W leads should be close to zero when in neutral.
I've wanted someone to read the color bands on the resistors for some time. If you throw yours out, please take it apart and come back here with the colors. I can help if you're not familiar with reading them. The following might be what some of them are:
1,500 : Br-Gn-B-Br
2,800 : R-Gy-B-Br
6,100 : Bl-Br-B-Br
15,000 : Br-Gn-B-R
There's also a 5th band that is Br.