Rebuild done, where to start with jetting?
 

Finally have a top to bottom rebuild done on a '88 XT600, I have a Lectron carb for it but I figure it best to do the initial startup on the stock carb. The last time this unit was running was in British Columbia at around 650m (2,000 feet) above sea-level, so I am assuming it was jetted for that altitude. Now we are at around sea-level, one size bigger? I am running a big-bore (96mm) 11.5:1 compression with a supertrapp exhaust. Where is a good place to start for jets?

Also have a MSD high performance ignition coil which fits very nicely in the spot where the stock coil goes, should give me a real nice snappy spark. I did this on a '76 RD400 (two stroke twin), replaced the stock coils with Delco automotive coils and I found I got much fewer fouled plugs, smoothed out the idle real nice too. My only issue is that the RD was a points-system (until 1980) and the XT is a CDI (I am running an aftermarket CDI, don't know which kind). Will there be any problems running a high tension coil on the CDI? I would rather not frig-up the CDI as they tend to be rather pricey.

I want to help you with your set up but I'm having trouble remembering what jets I have in my bike right now. The trouble you will have is finding jets for the stock carb here in north america, seem to be avaible in a selection of sizes over in europe thou. However small round main jets for a Keihin carb will fit but they may flow slightly diffrently than oem ones, not a big deal if your re-jeting anyway.
If I rember corectly, In the main carb I have a 140 main, 46 pilot, needle raised to 4th groove and the secondary carb the main is a 130 and the needle in the 2nd groove @ sea level.
With your set up it might need a bit more fuel but this should be a good starting point.

start with the standard or what ever you have in the carb at the mo.
Run engine under load ( up hill) in 3rd or 4th gear full throttle. Kill engine grab the clutch coast to a halt ( PLUG CHOP ) take plug out look at colour, if black too big main jet, white/ speckled too lean too small main jet. light tan coulor just right. (dont use new plug but one with about 500 miles on it.)

once main jet correct, set idle speed and adjust pilot screw to achieve fastest but constant tick over. reset tickover to correct rpm.
if you cannot get a good tickover you will need to try bigger or smaller pilot jets. if bike starts easy when cold with no choke, pilot jet too rich. if needs lots of choke and is hard to start then too small.

once all this is done ride bike and slowly open throttle to see if any glitches in rev range at different throttle positions. fine tune this by lowering or raising needle clip height.

Ok, found jets in a range of sizes here, just had to order them. Simply ordered a set the next size up for starters, if anything it's going to want more fuel than less with this setup. For now, I'm just trying to get the damn thing started with the original setup ( 130-both mains, 46-pilot ), all I seem to be getting is the occasional small backfire - no start. Everything should be in order: nice snappy spark, fuel, carb & jets recently cleaned, valve clearance, de-comp lever freeplay, the only thing I have yet to check is the fuel level in the float-bowl. Absolutely everything in this engine is new. Nothing but farty little backfires. What do you mean by: "tick over"?

tick over = idle speed

That's what I thought, just wanted to be sure. Cape Breton, I used to live in Antigonish haha! Is it possible that I'm getting way too much fuel, and it's constantly flooding? The plug was soaked with fuel when I tested the spark. I've been running diesels for so long I have forgotten the finikyness of air/fuel mixtures.