I need to manually turn the engine over a few times to check things such as exact pushrod length via the expo marker test and a couple other things
however, I would rather not disconnect the battery if I do not have to because I have already put 40 miles on the PCM since the LE1 swap and the car has gone through a good deal of learning.

Is it safe to turn the motor over by hand as long as the key isnt in the ignition, or is there a chance it might fire up and break stuff and my arm

 

You should always disconnect the battery when working on the car. But if you're afraid it'll fire up (which it won't) just disconnect the coil wire.

 

If disconnecting the battery is going to make a large difference in engine operation, then you need a tune.

 

The computer relearns the fuel trims very quickly after being disconnected. Also, a good tune should not be very far of the corrected values once the computer has "learned" the car..
If I disconnected your battery now to reset the computer and hooked it back up (without u knowing it) you probably wouldn't even notice a difference. And if you did notice a difference it would probably go away before the engine is fully warmed up

 

ok, thanks guys
I'll just disconnect the battery

 

It'll be a lot easier to turn over if you pull the plugs.

 

It sure won't fire up, then.

 

Make sure you use a lot of washers if you're turning it over with the crank bolt. I already bottomed my stock one out and had to retap the crank.