360 stock push rods length reusable

Maybe.....maybe not. What head gasket do you plan OP? That plays into the equation. If a .028" head gasket is used (which is close to stock thickness), then you'll lose pretty much all of that .045" from the available lifter piston travel, and with tolerances stackups, the odds are good of some bottoming out. If you use a kit Felpro head gasket, the the extra .020-.025" thickness reduces some of the lifter piston travel that you lose from the milling.

The above is just the head milling compensation. If a valve job is done, and the valves are sunk into the seats at all, then this becomes worse and compresses the pistons down in the lifters even more.

As noted, measure the preload in the lifter pistons... with that much milling and the tolerance stackups, you probably need to look at them all. BTW, the preload is from the OUTER ring under the retaining clip, not the inner circular thingy... (at least for the most common oil-through lifters...) And you look at each one when on the base circle (valve fully closed).

If this is a low buck build, then it is conceivable to use shims under the rocker shafts to compensate the height changes. The shim thickness is 2/3 times the pushrod length you want to compensate. E.g., for a .045" correction, use a .030" thick shim.
The head gasket is the thicker one which is .054 compressed, how would I check the clearances that would be after I torque the rocker arm shaft to 17inch pounds? I usually never check any clearances and it turn out fine as long as I don't go crazy on the lift, but I wanna get this done the right way and check everything. Guess I got a lot of reading do I need a dial indicator?