When you add a thin piece of wood for register sliders you should do that *before* you do tuning, because anything that comes into the path of the air/sound later will affect the tuning. The best thing to do is to first buy (or make) the register sliders so you know exactly there the holes need to go later. (The holes in the sliders may not match the holes in the reed block exactly because the register sliders need to not only open but also close, often requiring a bit more "closed" room than the reed blocks will give you between their holes.
I would start the woodworking process by first cutting out the long straight "indentation" the slider will rest on. You use a router for this for the best results. The indentation must match the width and thickness of the register slider rather accurately because once new wooden bottom is attached to the reed block (much later) the slider must slide smoothly without leaking air.
Then you copy the hole-pattern onto the new base, by first drilling holes that are too small and then you enlarge and shape the holes match the pattern, using a router. Do not use a drill to enlarge the holes as with the drill you would need too much lateral force and you cannot work with enough precision. The whole process requires quite a bit of precision and is hard enough with a router. It's much easier if you have access to a computerized mill. That is what accordion factories use, as well as some of the larger/advanced accordion repairers. I have no experience with this but I bet that achieving the right precision to combine a smooth working of the sliders together with having no air leaks is a real challenge!
Note that many parts can be purchased ready-made. You can buy a metal base with the long cut-outs for the sliders, the sliders themselves register mechanisms, switch tops (with markings), rods that go from mechanism to the "pass-through" (from outside to inside), that pass-through itself, etc... All these parts are pretty standardized, which explains why they look identical between accordion brands and models, and why because of this also the spacing between reed plates on reed blocks appears to be more or less the same as well.