Quiet thread... I only gave it such a boring name because I wanted to help out the newbs who actually use the search function. :yup:
Anyways, back to business. First order on the agenda piston to valve clearance.
So the four stroke engine cycle is intake, compression, explosion, exhaust... For two of the these events the valves are opening/closing with the piston close to top dead center. During intake, the intake valve opens right as the piston starts to lower (thereby creating vacuum and drawing in air and fuel). Then during the exhaust stroke the piston chases the exhaust valve closed (shoving burnt fuel out). Generally speaking from a power perspective it's a good thing do open the intake valve as soon as possible and leave the exhaust open for as long as you can. One common misconception I found was that lift has practically nothing to do piston to valve clearance. Your valvespring might not be able to handle 2" travel of a valve but thereretically you could have a valve chase a piston all the way down. It's duration that gets people into trouble. In addition to more valve overlap, agressive cams try to push the envelope in when you can open and close valves and how quickly.
Why do we care? The problem comes if you don't maintain sufficient clearance between pistons and valves which from everything I've read is 0.080" on intake and 0.100" on exhaust. Now I didn't really know where these magic numbers came from but I at least have a theory as to why they're needed.
Before we get to that lets talk procedure. Generally folks take one of two methods when checking piston to valve clearance: clay bar or dial indicator/feeler gauges.

For the clay bar method you lay a strip of modeling clay ~0.20-0.25" thick on the surface of the piston (head off), reinstall head, spin the crank over at least 2 times, remove the head and see how big a dent you made in the clay. For dial indicator method you replace a pair of your normal valve springs with checker springs (sometimes also called test springs). Then you find top dead center and manually drive the valve in further than the rocker would until it touches the piston. Check springs are weak so this isn't a problem. You then measure how far the valve had to travel either with a dial indicator or with feeler gauges between the tip of rocker and end of valve all while turning the crank over a degree or two at a time.
The complication comes because of the hydraulic lifters. Hydraulic lifters are by nature a two piece design with an internal spring. BUT this spring has a lower spring rate than do the valvesprings. Therefore if you turn the crank the lifter will compress before the valvespring does. This sucks because the valve doesn't move in and out normally and clearance can't be verified. When your engine is running normally there's an oil port on the side of each lifter and internal diaphram such that oil pressure assists the lifters in opening the valves so lifter collapse isn't an issue. What IS an issue is that as you rev higher the lifters can "pump up" to the point the valve opens further than usual hence the clearance you need...
If you ever take a lifter out of your engine it'll be fully extended with the pushrod seat all the way out to the stops. Looks like this:
This is not where your engine normally needs it. Your pushrods are a touch longer than the spacing between seat and rocker so the lifter starts with some nominal compression. This is preload and it's generally good to be in the range of 0.020 to 0.060" of lifter preload. The lifter actually stays in the middle of its possible travel and the oil displaces any and all slack in the system so the lifters run quiet and smooth. Pushrod length dictates preload. Period. Only if you have ajustable rockers and/or shim rocker height will the "wipe pattern" on the end of the valve change. A final note on pushrods: I ran into a tech article that warned that crappy pushrods can cause all kinds of problems because the shaft itself introduces another spring into the system. This is especially true as you start getting into stiffer valvesprings. That made sense to me so I'll be running comp chromoly pushrods.
Hydraulic lifters mean you CANNOT do the clay bar method without somehow making the lifter dominate the valvespring. You can buy and use and couple of solid lifters (which will dominate) or you can install check springs with the clay bar to ensure the lifter stays extended.
My route? I went and bought the check springs and used feeler gauges. The way I thought about it I didn't want to take even a head on and off twice if I didn't need to.
1) installed head, all lifters where they're supposed to be
2) installed check springs in place of the big valve springs
3) used adjustable length pushrods to give zero valve lash (which by definition means fully extended lifters aka zero preload)
4) found top dead center
5) checked clearances for about 20 deg before and after TDC.
A couple pics of the process:

Cleaning the gasket surface with a plastic scraper (the graphite is ANNOYING as all get out to get truly flat. I probably spent 2 hours at this.)

Used head bolts with a flat ground in them...

Are great for cleaning out the threads in your head (props to LS1tech for the tip).

My modded valve spring compressing tool. This was made for studs in either 5/16 or 3/8" and the ls1 uses m8 bolts. What to do? Make a shackle. I actually trimmed it a bit more to get the travel I needed.

valve spring undone

check springs installed

stack of feeler gauges. The piston is touching the valve here.
The bad news. I only had 0.076" on intake and 0.070 on exhaust. Less than 1/32nd of an inch screwing me over. Then again this was on a 243/252 duration cam which is HUGE so I knew it was going to be close. For comparison the T-rex is something like 242/249.
Options if you don't have the clearance specified? Normally you have 3...
-Adjust cam timing (not only am I loathe to go buy and aftermarket ajustable set, this actually won't work for me because if I make the exhaust better the intake gets worse and I already failed both)
-Notch the pistons (supposedly not too hard you basically insert a cutting bit shaped like a valve in the normal valve spot and cut to a known depth. As mentioned I didn't want to take my heads back off and I didn't know how you'd control depth and therefore weight removal).
-Run a different cam. This is me. I have one Futral F13 (230/232) now on order. It'll still be agressive, but a lot less so.
Interestingly you don't actually have to use adjustable pushrods. As long as you can figure out what the normal preload of the lifters are you know how much further than normal the valve gets pushed in toward the piston (it's just the oil pressure maxed out how far the lifter could pump up.) Preload is pretty easy to check you just start will your test rocker off and cam facing such that your not on a lobe. Be sure you give the lifter enough time to extend. Tighten the rocker down until there's no play in the pushrod but the rocker is not yet tight to iron. Then use a straightedge at the valve cover elavation and scribe a line in the pushrod. Tighten the rocker the rest of the way down which compressed the lifter. Scribe another line and measure the difference.
Here's my epiphany: Preload is supposed to be 0.020 to 0.060. If we take the max amount the lifter could pump up 0.060 and translate this into valve motion (times 1.7 for the rocker ratio) we get 0.102 which is almost exactly the 0.100 we're required for our worst case scenario exhaust valve. You can do this same calc and avoid buying adjustable pushrods if you don't mind a bit of extra math.
Finally a note on rockers. The only real weakness of the stock rockers is that they sometimes spill their bearings. A real roller tip rocker may be a hair more efficient but they're also heavier and harder to control. Plus they won't clear the stock valve covers and I don't want to run spacers for fear of hood clearance difficulties. My solution was to send my rockers off for the Harland Sharp rebuild. It's $250 for the service but the pivots are burly. Contact Nate at nastyperformance.com if you want them sent over.
Here's the result:

The pivot assembly is actually the same one used in Harland's full-on roller rockers. You can see a good side shot of the pivot and circ clip above in the pic with feeler gauges.
-Joel