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Compression loss and rough running.... Saga

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royhall:
For a rebuilt engine that's not yet bedded in they are pretty good compression readings, assuming that it was re-bored or re-ringed with a hone. I would swap the DynaS for a set of standard points if you still have them. DynaS has been plagued with failures that do look similar to this. Temporarily going back to points will eliminate the possibility of electronic failure.

Clem2112:
a bit more info...
It has covered a few hundred miles in shortish outings since the re-build,  during which time the carbs have come off a few times for float valve leak issues, new jets , floats too
 - to rule out those as the culprits !

A set of new OE points (with a DSS backplate setup) went back in this year to eliminate the Dyna ignition as a possible issue. Strobed too. No better !

The last time the head came off after about 500 miles, all four bores still had honing marks and looked very new (0,25 oversize on all 4) and the piston crowns had a sooty look but not too bad.

The cold engine readings seem ok to me too.... but the difference seems suspicious ie over 10% and 1-2 and 3-4 pattern.
Then the warmed up readings seem very weird unless there is something going on with
the gasket (no leaks anywhere around the joint either!)... maybe I have "over-thought" the possible reasons why ?

royhall:
Wow this is going to be a tough one sounds like you already covered most things.

Just a few thoughts. You say you strobed it, did you rev the engine with the strobe attached to check the advancer in case its stuck in one position? Also are you sure the coils and leads are okay, and all low tension wiring has good joints and is connected correctly. Also check the negative lead from the battery to the frame (earth) is making a good connection ie. clean away any paint etc under the lead and is the lead itself good. The symptoms sound like ignition problems of some sort.

Clem2112:
Think the electrics and wiring are good but I will go round these easily overlooked areas again just to be 100%.
Nice to think it could just be something simple and cheap to fix !!
Head off to find nothing would be frustrating !

btw the 12v feed to the ignition goes through a relay so I could bypass the old harness wiring (kill switch also "new" as I bought OE switchgear too) and ensure a healthy supply to the coils (new Dyna 5 ohm, new copper leads made up and sparks look good to me)
Advancer seems to advance and retard ok with the timing light to check it moves both ways freely.

K2-K6:
Just a quick thought, as Roy has pointed out and it seems you've got a fairly comprehensive view of the status of most current parts and setup,  have you read the MrT post on his 550 as it appears that his problem is coming from the dyna coils and has given him a right runaround in trying to get to the bottom of it.

They are fairly new in his case as well and have given some very strange symptoms, maybe worth a check with some other coils to at least eliminate something simple. He also has visible sparks with his.

Compressions, as previously stated don't seem bad and I wouldn't first suspect those as your cause. Regarding the hot reading being lower, it might be worth just checking the tappet gaps when hot, not measure them but open the caps and just rattle them to check if you've lost any space that could keep the valve marginally open.

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