Are all intake valves the same length? Now I'm worried the machine shop assembled it wrong after I had them cut all the valves. I know they did a bench pressure test to make sure there were no leaks.
On a motorcycle you DO NOT cut valves!
No wonder the tappet adjusters are different.
The valves are sitting in the seats at different heights.
You just install new valves and lap, thats it.
It must have been a car garage that did the machining.
They did not know any better.
What i would do now is just make sure all of the valves are adjusted properly.
Make sure the rocker arm is not contacting the top shim on the the valve springs.
Look for marks.
When you get that done, I would check the compression on #1 cylinder.
AS for the missing on cylinder #1....
Since it is a 1977 I would take the air cleaners off and with the engine OFF turn the throttle and make sure all of the nozzles are squirting especially #1.
If #1 is not squirting then i would pull the rubber fuel tube that goes from the accllerator pump to #1 nozzle and spray some carb cleaner through it.