3.5 hours is about right. It's hard to say about the shims without knowing what was there to start with.
Here's the 'Readers Digest' version of the work involved.
1. Remove the battery cover and disconnect the battery.
2. Remove the seat(s). (to get at the tank bolt)
3. Remove the fuel tank.
4. Remove the cam cover.
5. Turn the engine 2 full revolutions, stopping each 1/4
turn to check the valves and noting the clearance.
6. Remove the cams if the valves need adjusting.
7. Remove the shims as needed.
8. Inspect the shims for wear and measure the true thickness.
9. Calculate the required thickness.
10. Install the new shims.
11. Reinstall the cams.
12. Turn the engine over by 1/4's again to make sure of the adjustment.**
13. Reassemble the bike.
14. Start it up and warm up the engine, checking for noise and leaks.**
15. Take a test ride.**

** Anything wrong at these points means doing it all over again, usually for free.

As for possible damage, a lot depends on just how far off the were and which way. Tight valves will burn in short order. Very loose valves will eventually pound the cam faces and valve stems out of shape. I once worked on a Honda 350 that had a cam that had been hammered so badly that the hardened surface was flaking off.

Let's hope there's intelligent life somewhere in space 'cause it's buggar all down here. -- Monte Python