Check with your machinist to see what it will cost to set the the clearances via trimming the valve stems.
Add the cost of cleaning up anything else he sees.
Add in $200 or so for gaskets.
Figure on at least 2 or 3 weeks of downtime.
Ask yourself if it will all be worth it.
Even if you only have the one valve trimmed, you still need a gasket set, as you need to remove the head to get the valve out.
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Head is already at the machinist's shop - not charging me for the work since he admitted to 'flubbing it the first go around.' I asked him if he knew I'd have issues with the new seat; he acknowledged this and told me he had forgotten to cut the valve back - like he told me he would - to compensate for the new seat. So, good news there at least.
Gaskets are basically free. The Valve cover gasket is a realgaskets reusable silicone gasket that I've been using for over a year now. As for the head, I won't need to buy anything extra - I do actually keep backups... two of them are sitting in the cabinet. (I got lucky and bought a 'lot' of 3 MLS gaskets for $60!)
Discussed cutting new threads for a camshaft cap and one of the exhaust flanges. Said it should come in under $20 for both. Not too bad all things considered. Said everything else looks good... For now.
Panic and rage over a little bit of mechanical work?
'Little' here is an understatement of immense proportions. To get things started, the bike has sentimental value. It is what my brother and I learned to ride on together before he passed. Aside from that, back in February of this year the bike was crushed by falling debris while I was at work, damaging damn near everything but the frame and engine. After a lengthy argument with insurance companies, they agreed to completely rebuild the bike.
I took the cash, put it into a lot of updates and upgrades, paint, etc. As it stands, the bike represents hundreds of hours of my own labor this year alone. I started over with a complete stripping of the frame and engine, and worked my way back up. I didn't catch the issue with the head until I was well over halfway through with the rebuild.
By the time I learned that the valve tolerance was fudged, it had been 7 months of work, stress, and worry over the engine. So... rage was my first reaction, yes. I've been using my spare time to work on friends' bikes as well - having just completed a 750 rebuild for a friend, and am starting a gl1100 for a neighbor. At this point I'm getting so sick of tearing engines apart I wanted to scream when I found out I had negative clearance on that valve. This, after tearing off the wiring harness and replacing the ignition signal wires(necessary, one had corroded through), the coil wires(not necessary as it turned out, but yielded a voltage bump), tearing down the carburetors and dipping them - thoroughly dissecting and cleaning them, and triple checking my engine timing trying to figure out why in the hell #1 wouldn't fire.
When I realized what was wrong I was furious, as I've said. Only reason I didn't even think to check compression is because the piston wasn't cracked, the rings are brand new, and every other cylinder was firing... I assumed it was a spark, air, or fuel issue.
I couldn't find my compression tester, so I just stuck my thumb over the spark plug hole and it felt like someone was weakly blowing against it as the engine cycled.
Rage, yes. If I had thought the check compression first... ugh.
Steve, good points, but I hopefully assume the head was not reinstall prior to checking the work and clearancing. If it was........!!!
It certainly was

however, no damage seems to have resulted from the negative tolerance. It was run maybe 30 minutes total since full reassembly till I realized where the problem was.
The valves were all shimmed last year (or two years, I can't recall)... And no, sadly I 'flubbed' (to quote the machinist) when it came to double checking the work. I assumed he'd cut it, like he originally told me he would. I should have expected the worst when he told me he forgot to cut the threads the first time around. Bah. Live and learn, I guess. I'll be checking every damn shim again before I finish reassembly. I cannot stand being so close to being done, only to have issues like this pop up at the last minute.