Tappet clearance/timing question on 1973 Honda CB350

Hello all-

I'm new to the forums here, and I'm hoping you guys can help me out.  I had to basically rebuild the top end in my 350 motor last year to replace the pistons.  It used to be my fathers bike and the rings stuck on him- he managed to break them loose but when he did it deformed the grooves in the piston and we had to replace them.

Anyway, after getting that taken care of, I can't seem to get the tappet clearance properly set.  I know how tricky it is to do, but the main issue I'm having is that there's absolutely no clearance between the tappets and the valves, at all.  It's not like I'm not getting enough clearance for a feeler gauge- there's just no clearance at all, except on the #1 intake- the other 3 don't clear.

So I was fidgeting with it again today- I have the motor out, the top cover off, and I can see the cam and rocker arms.  I noticed a few things-

1] The timing mark on the cam sprocket does not line up perfectly parallel with the top of the case when the generator "LT" mark lined up with the index mark.  It was leaning right, so I tried jumping the chain a tooth, but all that did was tilt it back the other way.  So the line either leans right or left depending on which way I have the chain set.  The only thing I can figure on this is that the cam chain has stretched a little.

2] I made the rookie's mistake of not marking everything when I pulled apart the top end, so when I went to reassemble, it was kind of a guessing game with the rocker arms and shafts.  At the time I didn't think it mattered too much and put things together and managed to get it running well enough to get me thru the last few weeks of summer last year.  The same with the rocker arm shafts.  Now that I have things apart again I noticed that the rocker arms are stamped with numbers, and I think they're there for a pattern, but I'm trying to figure that out.  Each arm has the number 312 stamped on it on the cam side, but on the valve side they each have different numbers.  Two have a 1, and the other two have a 3; but then one of them has a 1 point, and the other a 3 point.  So basically, if you had them laid out, it would look like this: 1-1*-3-3*  I hope that's clear enough to understand- if not maybe I can get some pictures posted.

Anyway, after all this explanation, my question is does the position of each rocker arm make a difference in being able to adjust tappet clearance?  And if so, can anybody tell and/or provide me on how to determine which arm goes to which valve?  The same with the shafts- does each shaft have a certain position, and how to determine that?

Also, what do you think about the timing mark on the cam sprocket not lining up perfectly parallel- does that make a difference?

Thanks so much in advance for your help.
-Brian