no problem. it always helps to ask questions, even "annoying" ones
you don't have to use the micro usb that is on the psu (or at all). that makes it convenient when you are building, to power it there, but there are also inputs to allow you to put a connector somewhere else, which i almost always do. you can use a "barrel plug" type connector and use the original hole, so you don't have to open it up. or, you can do something like mounting the psu in the cartridge, with the charging port there, and stick a button in the original hole.
for "safe" shutdown, you need some kind of gate, or something to handle telling the pi to initiate the shutdown, keeping it powered, and then telling the psu to cut the power. the pocketadventures.com power assists have a way to do it built-in, but i don't know how well the pro board (that has the volume and usb as well) would fit with the tinkerboy dpi adapter. it might be ok, but i've never done that, so you might run into space issues. the basic one is great, and fits in a printed cartridge.
helder's psu doesn't have a "safe" shutdown option, but you could put a tactile switch somewhere to initiate it too, and then just cut the power when it's done. his "one-for-all" scripts can handle for that I think, and his has a battery monitor option built-in too, which is nice (and the power assists don't have).
camble also has an option, that is technically made for the adafruit powerboost, but can work with just about anything, if you don't care about its low battery monitoring option.
for the shoulder buttons, some people do a six-button face layout, which the v3 board does, so you don't have to mount anything anywhere else, or you can put them in the rear. there are a number of brackets available in the 3d printing forum here, and on thingiverse, if you just look for "gameboy zero". there are lots of options there, with "clicky" tactiles, mounted button boards/pads, "soft" tactiles, etc. my personal favorite is to mount them where the middle screws normally go (like in wermy's original build), but to use my 3d button or insert design to have a full-size button there, and use soft tactiles mounted on the screen bracket (usually using sixteenbit's design from thingiverse, or a derivation of it). the builds i link in my signature have some examples. the most popular (just above the battery) has lots of options, but it's not my favorite, since it means you can't lay the gameboy down without pressing the buttons. tinkerboy has a bracket for sale on his site too, for mounting tactiles off to the sides, and pocketadventures has one for the above-battery option.