Engine/Transmission (1994 - 1998) Haisley/Scheid Stud kit Questions

[FordCummins]

I am currently installing the standard size (12mm) stud kit, and have a few questions. Some of the studs seem to run into the block further then others, with some studs having 2-3 threads left showing as they bottom out, and some having none showing when they bottom out? All of the studs seem to turn very freely, and all of the sudden tighten right up, which leads me to believe they are all bottoming out correctly. Is this just a variation in machining? Also, why do the instructions say to check and adjust the valves with the engine hot? Its contrary to what the Cummins service manual says of checking them when cold. It also says to run the motor with the valve covers off, wouldnt this make a HUGE mess? Thanks for the help guys.