Welcome to the site !!
We need to clarify some things so we can see if there is anything you missed ......
First ..... You said you recently adjusted the valves , and now are having issues with it starting ....... Was it running/starting fine before the valve adjustment ?? , or did it have the same symptoms before the adjustment ?? ....
You also said the timing marks are not in alignment when checking each side .... where are the marks on the Cam Sprocket when this is taking place , are they both level with the head and the cam lobes facing 2 O'clock towards the rear ??? , and if so , which of the other 2 marks are aligned when the cam sprocket marks are level ?? , if it is the clutch side , then I would say you are 1 tooth off , if it is the ignition side , then I would say the timing chain is stretched ...
So most likely the Timing Chain is stretched , OR when you did the adjustment you got the timing 1 tooth off ...... if you are confident the valves are in spec , then timing would be the issue , if the lash was below 0.004 then I would say the issue is the valves are toast (Intakes) and need replaced .... which would also explain the lower compression , if the valves are not seating , your compression will be lower ......
All 3 marks need to be aligned , the 2 on the cam sprocket should be level with the head like this -o- , the timing mark in the small round hole , and the dot/triangle on the clutch side , ALL 3 need to be on the marks , if not it only leaves 2 possibilities , either timing off 1 tooth , or stretched timing chain ..... Report back with findings .... and/or add any info you left out as I mentioned above ......
Backfiring is a sign of timing off , or a valve open/not seated/worn ......
On a related note , once the valves start moving , then it is only a matter of time before they go again , or completely , and you will need to do a valve job , you may get 1 ride out of them , or 50 , there is no telling when they will zero out again , once you get to the smallest shim , then you are done adjusting and have no choice but to replace then or the head .... if you are not racing , then I would suggest going to Stainless Steel Intakes , you will lessen the need for adjustments and replacement by 2 to 5 times or more depending on what you do with the bike , if just play riding , you could get 10 years out of them before any adjustment is needed