i'm not the greatest woodworker in the world, but am currently trying to do the same thing laminate over everything.
i recessed my trackball maunting plate and my analog flightstick 1/16" into the top of the cp.
my competitions i sunk in 1/4" on the backside of the cp then drilled the mounting holes and hammered in some 1/4" threaded inserts into the mounting holes. they are 5/8" long plus the 1/4" routeded hole comes out to 3/4" exactly giving me a flush surface on to to laminate.
the trackball is even easier just routered a 1/16" hole the rough size of the mounting plate, screwed it into place and laminate over it, then i just took a hole saw the same size as the mounting plate hole and cut it out
.
i drilled all my buttons and joystick holes 1 1/8" just laminate over the whole thing then drill pilot hole through all of these and take your router with a laminate finishig bit and router all your holes, they will come out nice and neat...and perfectly aligned.
the restrictor plate i got from oscar pased a bit of a problem as i was planning to cover it as well, but, they have like a 1/64" dimple over each mounting screw that i didn't feel like dealing with , so it is just surface mounted it. i bought all the black dimpled plates from oscar, and since my cp i all greans blacks and dark greys, it fits perfect.
the other problem i ran into was my flight stick...i couldn't think of a reasonable way to cover the carriage bolts for it and laminate over the entire thing, so i compromised, i'll laminate over the plate except for a circle about 2 1/2" wide where the stick comes through the mounting plate and run the carriage bolts through the laminate, probably will enamel them green to fit the cp unless i get black bolts instead.
hope some of this might be useful to you, and maybe someone greater and wiser than myself will reply