Shucks, those aren't questions for the experts, they're for the newbie
RE 1: Clamping can be a tricky issue at times. You can pause your program and move a clamp. Do not release them all at once and the part should stay put, providing you use at least 3.
Many guys doing router work will attempt to hold the material down with a vacuum ported table, or whatever, in order to avoid the nuisance of edge clamps.
RE 2: Differing tool lengths is a common concern with multi-tool programs. Nearly every machine control in existence uses a tool length offset register (chart) in the control, which contains a measurement that the user determines is the difference in length between the master tool (Tool1) and each subsequent tool. This measurement is automatically applied when a tool is loaded, and the relevant tool offset is recalled from the offset register.
RE 3: If the spindle motor is variable speed, and has a drive amplifier capable of receiving input from the controlling software, then the motor can be run at user specified rpm. For the hobbyist, this may be an unnecessary expense, and he could simply use some sort of manually operated speed control. A pause can be inserted into each program, after a tool change, to allow the user to adjust the speed before continuing with the execution of the program.