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Can't get ignitin 180-degrees out, unless you carved new key-way in flywheel to flip it.

Ok, ignition/spark's clue there. If you've got spark, then you can ignore BAS, it's working. Safety interloc switches would disable starter, and that's working, so we can ignore those.

but there were a couple unused plugs I can’t identify in the wiring schematic
Post photos of these connectors and wire-colours. May be something important.

I have an ignition delete on this thing. So, not sure if this is normal.
Did you install this or did it come with bike?

As test of fuel-system, use squirt-bottle and spray 2-3cc of petrol into air-box, wait 30sec, then try starting.

 

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Another thing to look into is WHY it had blown headgasket. This is usually just side-effect or symptom of real problem. Any of these can cause blow headgasket:
  • overheating - test every component of cooling system, measure temp where thermoswitch turns on fan.
  • too much ignition advance
  • too much compression
  • too little octane in petrol for compression and ignition advance used. It's dynamic compression we're looking at. It's possible to adjust stock cams to point where dynamic compression is higher than available octane.
  • too little fuel-flow, can be fuel-pump, FPR, fuel-filter, injectors
  • too little fuel-pressure, same as flow issue

All of these can be tested and numbers gathered to compare to standards in manual to determine if they are good or not. Without numbers, you have no idea if it's correct. Find actual CAUSE of blown headgasket and fix it. Otherwise, it'll blow your new headgasket just the same.
 

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if concern is firing sparks out of order, simpler to just unplug connectors on coils and swap them.

Not firing on starting-fluid would indicate you've got sparks issue.

Low compression readings can be from several sources. If you used tester that had relief-valve near gauge, entire volume of hose up to valve is added to combustion-chamber volume. This will lower CR. More accurate to have relief-valve in tip of hose as close to cylinder as possible.

Other issue may be damaged cylinder bores. Depending upon how long bike was run with blown headgasket, coolant in oil will damage all surfaces needing lubrication. Most troublesome are cylinder surface, which is Nikasil coating on top of aluminium. If coating was damaged from lack of oil, it would be scored and worn off. Leading to lack of ring-sealing and low-compression. Rings themselves may also be worn. Did you inspect cylinder bores when you replaced headgasket?

Get DTC error-codes from ECU. It may have flagged something that's easy to rectify. Or errors may even be preventing ECU from starting bike. Look up up how to retrieve codes from dealer-mode-1 and dealer-mode-2. Codes will point at areas to inspect closely.

Good luck! :)
 

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Can you explain how this is possible? I was not 100% confident when I put the cams/chain back in, because when cams were placed EXACTLY as manual pics show (orientation of the "EX," "IN" and the lines on the sprockets at 2T - Cyl #2 at TDC), there was the slightest pressure on the Cyl #1 exhaust valve. This caused the replacement of the exhaust cap to be impossible without rolling it back a bit to eliminate pressure.
Yes, cam-gear marks line up with top of head at TDC to make it easy to check cam-timing. Due to lift curves being longer than 180-degrees, both intake & exhaust valves will be slightly open at TDC on exhaust stroke. Yup, to measure clearances, you have to rotate cam-lobes to aim away to get to zero-lift section.

It's possible to advance exhaust and retard intake cams so there's less of this overlap at TDC. This increases dynamic compression, but won't register on compression gauge since flow-velocity isn't very high. Will end up needing higher octane and some ignition/retard.
 

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How would I tell if this has been done???

I don’t think I explained that last bit well. The issue I had was installing the exhaust cam cap while the cams were positioned as shown in the manual, with cylinder #2 at TDC compression stoke. Specifically, the drawing shows the cylinder #1 exhaust lobe at aprox 7 o’clock. But in reality, when all marks, lines, EX & IN etc were as shown, the lobe seemed closer to 6:30 o’clock, putting the slightest pressure on the cylinder #1 exhaust valve lifter.

This would require pushing the lobe further into the lifter to get the cap to seat (probably could t do it by hand even if it wasn’t a bad idea). Or what I did, which was roll the crank a bit to remove the pressure. This allowed me to install the cap. Roll back and double check that all markings were still correct. This was checked again after the tensioner was installed. All looked exactly as it does in the manual.

Does that make sense? It certainly felt wrong when I was doing it. But I saw no other way to get the cap on.
You did fine! Need to install those caps very gently and evenly. Otherwise you can actually snap cam! :eek:

Only change I would make is spin engine forward in one direction only. There's some slack in chain and spinning it back puts slack on forward side of chain and can throw off timing marks.

Not likely your cam-timing has been adjusted from stock unless you see adjustable cam-gears. As long as timing-marks line up according to manual, you should be fine.
 

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Thanks again for the detailed response!



This was my plan, but it was the plugs/wires I was concerned with. They are tight (cyl #2 shorter than Cyl #1). Worried I might have caused damage pulling on them. I will see if I can free up some slack and get them to reach.



The relief valve was in fact near the gauge, on the coupler that mates hose to gauge. Unfortunately, both testers I have are like this.



I looked at the top of the cylinder walls when I had the head off. Never removed the jugs, so I couldn't see the entire stroke. The walls looked OK. Some build-up near the top combustion area. One cylinder measured very close to outside tolerance. When I get it apart I will get measurements of everything, and hopefully this highlights something obvious.



I tried to get codes from the Dash, but following the instructions in manual never started the described sequence. I figured this might be because there is no ignition? The procedure starts with the ignition, and I only have a kill switch (on/off wired to the ignition delete linked above). I was down the dash rabbit hole a while back fearing the dash might be damaged from removing it and not having it sit perfectly upright. But it now seems to be acting as it should, other than the lack of test-mode.

Going to be doing a leakdown test soon to see if this provides more info. I report back once I have some solid data.

...I'm going to need that luck! :)
I've used their ignition harness on my 250 race bike without any issues. Let's double check:

1. key ON, measure voltage of grey wire where it entre ECU connector (ECU connected)

2. key ON, measure voltage of each wire at ignition coils (coils connected).

It really does appear to be ignition issue since it doesn't run on starting-fluid.
 
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