The trick is to not rely on the plasma cutter for all the small holes.

Recommended method:

1. Cut the outer contours with the CNC plasma cutter.
2. Cut all large holes and openings with the plasma cutter.
3. For smaller bolt holes, only mark or pierce the center position with the plasma cutter.
4. Drill the smaller holes afterwards using a drill press.
5. For matching plates, first make one plate carefully. This will become your template.
6. Mark and drill 4 holes as far apart from each other as possible. Drill these carefully.
7. Place the template plate on top of the next plate and insert bolts through the 4 reference holes.
8. Check that the outer contour feels aligned and correct.
9. Tighten the 4 bolts with nuts so the plates cannot move.
10. Now drill through the finished template plate and into the next plate.

This way, the matching plates will have the same hole positions relative to each other, which is more important than every hole being perfect compared to the drawing.

If all holes are shifted 1 mm in the same direction, that is usually not a big problem.

But if matching holes are at different heights from plate to plate, the machine will be harder to assemble and align.

So the best approach is:

Plasma cut the shape.
Plasma mark the holes.
Drill the first plate carefully.
Bolt the first plate to the next plate.
Use the first plate as a drilling template.

Laser or waterjet is still the best option if you want the cleanest and most accurate result, but for a low-cost DIY build, plasma cutting plus drilling can be a very useful method.

I have used a similar method myself before, and it worked well.