To save typing it all out again here's a copied post I put on our less numbered Brittany Club site. Any help with diagnosis would be a great help.
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After taking just about everything off and apart it has to be step by step to ensure there's no major fault. Last week I had the water leak from the rear coolant supply pipe for example. Well, all is back together. I'd checked for leaks during the week so the alternator and starter motor went back on. The alternator is a joke! Haynes (or Kawasaki) says you need a special tool and two torque wrenches to tension the belt. Come on! Would you do that for a car engine? Anyway some sensible tension applied to the belt and then fixing nuts torqued up.
I had the spark plugs out so I could turn the motor over to get the oil splashed around. That done plugs back in, carbs on and cabled up. I jumped the battery from the V-Strom to be sure of good power (the old GPX battery was easily weakened just turning the engine over). New connection pipes to the tank, fuel arrived after a couple of turns and the noisy motor started on choke, eventually no choke and idling OK. A few minutes passed while the engine and exhausts heated up giving of some smoke and odour. After the mist around the engine cleared all sounded smoother with oil circulated to where it should be, hopefully.
No leaks below, oil or water,
Oil pressure light went out quickly, that's fine,
Fuel light on as there's not a lot of petrol in the tank,
Exhaust and headers sealed so it sounds happy,
Clutch operates fine, get first gear but won't lift enough to get second etc. I've got the linkage mal-aligned (I had the gears before btw),
Water heats up and a leak appears around the thermostat housing/filler/hose clips (it stops when the expansion overflow dries but needs looking at),
Radiator fan cuts in after about 15 minutes running, it wasn't connected when I first dismanteled the bike,
Throttle is fine up to 4/5K but after it wants to stall other than slow operation of twist-grip, it also has over-run with the throttle shut down. Thoughts on that one....experts please?
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Gears are fine now btw.