The cam chain is 94 links I think, so with a 30T cam sprocket , the link will move by 4 teeth every revolution. The math may be out but you follow what I'm saying.
Yes it is possible for the chain to jump a link when the motor is being assembled.
Your thread mentioned machining the block for more compression. How much came off?
Either way, I'd pop the head off and have a peak inside, or borrow a borescope.
1962 Superhawk Restoration: Here I goAll that was done machine wise, was honing the cylinders and having the gasket surfaces recut. Unfortunately, I don't have access to a borescope. Sounds like a wonderful tool though. I'll just have to pull the engine. Might as well now since all that's left right now is the frame and engine.
Current restoration: 1962 CB77
http://www.flickr.com/photos/1962_cb77_restore/ After a great deal of labor in stripping, scrubbing, sanding, and filling... the old engine cases were ready for primer. (see before photo) More importantly, replacing the previous owner's improper right side crankcase & kickstarter, (which was for a CL77!!) with the forward kicking CB77 crankcase, lever, and gears. Here they are drying out in the sun after three coats of Dupi-Color's engine primer. Rated up to 500°f.
Click image to view larger.  Current restoration: 1962 CB77
http://www.flickr.com/photos/1962_cb77_restore/ So I pulled the engine to take a look at what could have possibly been causing the odd noise. Looks like the master link is top dead center still. There weren't any marks on the pistons or valves to indicate contact.
Here's a link to the video with the clicking sound for anyone that'd like to take a listen.  I found that the left exhaust valve is open about 3mm at TDC. It shuts when the cam is moved just past TDC. Is this normal? There's a few times throughout the rotation where each valve will stay open about that amount for a moment. Should the valves pretty much be open/shut or are there a few instances where this is expected throughout it's revolutions? A friend noticed some blue smoke coming from my left exhaust, I'm wondering if this is the culprit. Does this indicate an odd shape in the camshaft? Note: I had a mechanic who specializes in vintage Hondas take a look at the top when while I had the heads bead blasted. He stated that the valve springs didn't need to be replaced, he just re-strectched them. Does this sound taboo? Cam and valves were reinstalled and set by him as well.  Current restoration: 1962 CB77
http://www.flickr.com/photos/1962_cb77_restore/
Where is the timing mark (T) on the rotor when you took this pic?
Check for the neoprene/rubber on the bottom of the advance weight prong. Check for the rivets which hold the sprocket being loose and allowing the sprocket to move in the assy. I found that the left exhaust valve is open about 3mm at TDC. It shuts when the cam is moved just past TDC. Is this normal? There's a few times throughout the rotation where each valve will stay open about that amount for a moment. Should the valves pretty much be open/shut or are there a few instances where this is expected throughout it's revolutions? A friend noticed some blue smoke coming from my left exhaust, I'm wondering if this is the culprit. This is normal and I wouldn't be worried about the smoke as the engine is attached to used pipes. (right?). ...............lm
LM is right on target when he asked about the crank position. The cam link will be wherever it happens to be. I don't always put them on top, sometimes they are one or more teeth off.
What is vitally important is that the cam is in the right place when the crank is at TDC. With the head off, we can't tell, but do you remember where the cranks was positioned when that picture was taken? SMOKE The motor should not be smoking out of the exhaust. If it's a slight puff from time to time it's probably an oil ring not sealing properly or a worn valve guide. Those motors rarely smoke if at all. Smoking on one side is a sure sign that something is not as it should be. Valve at TDC I don't have a valve plot for a standard cam and the performance cams have a lot more overlap at TDC, so the lift curves I have here have exhaust valves at 3mm or more at TDC on overlap. The mildest cam I have a lift curve for is the race kit "20-40" cam which only has teh exhaust about 2mm off the seat at top dead. If you rotate the camshaft slowly the exhaust should open and close smoothly and just before the exhaust closes, the intake should start to open. The exhaust continues to close as the intake opens. Those opening and closing actions should be smooth. There should never be a lag with the valve stuck open and then suddenly clicking closed. Valves should close noiselessly and smoothly. If a valve is hanging up and then slamming closed, there is a burr on the valve and it will destroy itself the rocker and the cam if you are lucky OR the valves head and piston if the valves tangle. I would double check that, and if it is hanging up, strip that valve out. I would not recommend that you send it back to the same mechanic. SPRINGS You might get lucky but I would never stretch and old valve spring to avoid the cost of new springs. I'd recommend a set of springs from R&D. they don't add a whole lot pf valve seat pressure but do allow the motor to rev without valve bounce.
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