^^^^ Just be careful not to poison the patient. Even good medicine can be toxic with excess use and mixed with other medicines. Get it running, ride it and evaluate your FJRs condition and try one thing at a time and note how your FJR compares to the baseline after the the action/change. The FJR is pretty bullet proof so the issues are likely to be minor.
It's just a thought but worth mentioning. The valves were loose which can almost only happen from an adjustment and the bike is in the range of needing the second valve adjustment so it is likely someone was 'in there'. It is common for even professionals to get the valve timing wrong by one or two teeth on the
cams and the FJR will still start and run, but may not start easy and will not run strong. If the crank sprocket was off a couple of teeth you would be looking for a new cylinder head. I know you have just done the valves, the valve timing may be what caused the previous owner to think something was wrong with the bike and mistook low compression as the root cause.
Time to get in some baseline riding