To affix the degree wheel, I stacked some washers under it then held it with the stock magneto rotor bolt. Leave it just snug until you find true TDC then smack it tight enough to spin the engine without moving. When you're playing with the timing, but SURE to use a tight fitting socket on the bolt and a breaker-bar (rather than a ratchet) because you will have to exert effort to open the valves as you turn the crank....but once they go over TDC they'll push the motor ahead with a surprising amount of force if you're not ready to control it. You have to ease it down because you'll be checking at .050" (or some other distance when finding Lobe Center) and if you let it jump ahead it'll totally mess up your readings.
You need the dial indicator to be moving as the cam follower (bucket/tappet) moves and this takes a little ingenuity as there's little space and you'll need to fab up a bent yet thin rod to get to the edge of the follower without getting hit by the cam as it spins. CAN be done...you'll see.
I got a set of dial indicator ends of differing lengths and shapes and found one that fit in OK...just be careful.
The 'decompressor' is only on one exhaust valve, so just put the dial indicator on the other one for a true reading of the centerline.
When you put the cams back in, you'll be trying to get them back in time (of course) but be mindful of which way you were trying to move them and take that into account with the relationship of the line to the head surface. If you move it...it'll no longer be exactly level...but that's what you want!
It all makes a lot more sense once you've got things set up and are trying to do the job. You might make mistakes and go the wrong way at first, but you'll get the hang of it and by the end of the day you'll be in control. With adjustable gears, I worked on mine for an entire week of evenings after work and finished it up on the weekend. Yes...I AM slow.
But I was trying to hit within .1 degree and found this difficult to accomplish...both making such tiny adjustments and then accurately varifying them with the degree wheel. You'll see...it's tricky! And again...you MUST maintain total control of the crankshaft rotation to do this so be sure to have a tight fitting socket and bar to fit the crank bolt.
Junkie is of course right...the valve clearances won't change just from cam R&R, but when you radically alter the cam lobe positions it's always good practice to check the piston/valve clearances just to be sure you're safe. My cam timings ended up being dictated more by what P/V clearances I was comfortable with than a degree setting that I was trying to hit. The farther you can advance the intake valve the better...but if you get too greedy you can shove the valves into the piston as it's rising to TDC...and that qualifies as BAD. A 'happy place' to be is something that the 'Old Timers' always talked about ....having the intake valve 'chase' the piston down the bore. When you get the timing just right, as the valve opens the clearance to the valve will not change as the piston is moving at the same speed until the valve is near full open. Watch for this when you're adjusting things...the engines run good when set up like this. And on mine...it came at 106 like Mr. Schmidt recommended so perhaps that's why the engines like this setting.
To check P/V clearance you need some way to lever the valve open and you can either fab up something on your own or buy the special tool that can reach in on the edge of the bucket and push the follower down until the valve touches the piston. You do this for the upper 30 degrees of rotation before and after TDC until you get a feel for how close you are. Without milling the top off the jug or the head surface you 'shouldn't' get into P/V clearance problems...but it's still good to check!! With TLR Wiseco pistons and .020" milled off the jugs, .005" off the heads mine was starting to get a little cozy so I was happy to do that extra little bit and check the P/V clearances. Peace of Mind.
Another reminder...keep total control of the crankshaft!!!! I know..you said that already, but if you let it snap ahead on it's own....and you've moved the cams perhaps too far (you won't really know until you degree them afterall) then the possibility of piston striking valve is VERY real. And they won't tolerate much contact without bending....which is BAD. Be careful and it'll be a wonderful experience and the engine will RIP!! You just don't want to damage anything while doing it. Good luck!