A few things about building machines from wood.
There are some serious issues that need to be addressed, whenever you need to attach metal parts to wood. Because wood is soft, any bolts holding parts in place will pull themselves into the wood. The more you tighten them, the more they crush the wood. Even the parts themselves can crush and dent the wood, causing misalignment, or parts coming loose over time.
The main way I solve this, is by using phenolic plates and inserts bonded to the wood. All the linear rails are mounted on phenolic surfaces that have been epoxied to the wood, then CNC machined flat, with straight mounting ledges. This gives me straight, flat surfaces that won't crush when screws are tightened, and automatic alignment of linear rails. How to actually bolt the rails to the wood is something I've given a great deal of thought to over the years, with a lot of different ideas.
I've thought about bonding steel plugs in from the back, and drilling and tapping them. But that's very labor intensive. Note that this build is very labor intensive. I'm not averse to lots of extra work, but I really don't want to drill and tap 200 holes, that need to be accurate to much better than 0.5mm.
My other thought was to bond some type of steel nut into a pocket. My concern there is with the nuts not having a firm enough surface to hold them still. The other day, I had an idea that I'm going to try. from the back side, I'm going to bore 3/4" holes to within about 1/2" of the phenolic plates. Then I'm going to epoxy in 1/2" lengths of maple dowels. This way, the nuts will tighten againsdt the maple endgrain, to resist crushing. I'll pour some thin epoxy over the dowels, to soak into the end grain and make it even stronger, then go back and rebore the holes to give me a clean flat surface for the nuts.
The rails use 5mm bolts. To locate the holes, I found a drill bushing that's very close to the counterbore size in the rail, that accepts a #8 drill bit. This gives me a small amount of clearance.
I'll clamp the rails in place, and drill the end holes, and bolt them in place. Then go back and do all the other holes.
I'm using nylon locks nuts on the back. When all the bolts are in, I'll flip the part over, and pour thickened epoxy over the nuts, to hold them in place. The nylon should seal the epoxy, and as long as the screws are oiled, they'll come out fairly easily.
This will be a fairly long process, so I hope to get started soon. Just need to get the garage cleaned up a bit to make more room to work.
Here are some pics of my gantry parts to show a little of what I'm talking about. Looking at the dates on the pics, it looks like I cut them 7 years ago.
The gantry is roughly 8" square, and about 67" long. It's a 4 sided box, with each side being 1" thick laminations of 1/4" MDF. The MDF was laminated in my vacuum frame press, with plastic resin glue. This makes them very stiff and rigid. I did some calculation years ago, and cam up with a max deflection of about .001" with a 20lb load. I believe that in reality, it will actually be even stiffer.
If you're wondering why I used MDF, it's because it was free.
The beam will be epoxied together, with bonded in fasteners. It will be mounted with studs that are bonded into the beam, all the way into the internal ribs.