Ok, I was bowsing the web and fell across this posting about your bonnie head
The last time I rebuilt a bonnie engine was back in 75 so I may be a bit rusty on the subject.
I am from the UK and owned and worked on bonnies for a living and without knowing the year of bike I may get things a bit mixed up
The copper head gasket MUST BE clean of all grease , oil and any other debris such as carbon deposit, as must the mating faces of the head and the barrel
The old style of doing this was to soak copper gasket in parrafin then wash in petrol and wiping with a soft non abrasive cloth.
The next stage is to anneal the copper (I dont know if you have done this or not, but will explain anyway)
I used to use my mums gas cooker (much to her displeasure), the trick is to heat it to a dull red colour, If you are doing a copper gasket as opposed to a washer, such as a cylinder head gasket, some people like to cool by quenching in water.
Drop it in edge first for quick, even quenching. Quenching isn't strictly necessary, the rate of cooling makes no difference to the resulting softness.
If the head gasket is soft, you should get a good seal, but ensure you undo and re-tighten (to correct torque) cycliner head bolts in the correct order so as not to warp the head.
You also mention a rebore?, I assume you have fitted new plus size diameter pistons and not used the old ones, if you have used the old ones this will cause knocking problems , oil leaks, loss of compression and damage the engine assuming it even fires up that is.
skimming a head will increase compression, and the bonnie has a variety of pistions.
7:1 on later models and 8:1 on earlier. however, some models were fitted with 11:1 which had a castle dome with big cut recesses to allow valve clearance, these were mainly used by speed freaks and racers and really upped the power, but also blew alot of engines
(that would be me), I changed back to 8:1 after that.
To be continued.