Hi MH _ going thru this point by point
1) Look up the manufacturers specification for the rail foundations that's the starting point
2) good idea to have them cut in one setup
3) can do it one at a time if the machinist is good and can register one side to the other somehow
4) top and bottom is good if you can machine the rail foundations to keep them parallel and square
5) ends could be improved, do you have access to fea? as that gives you clues to what is compliant and what is OK
6) thicker plate is better for local stiffness. Depending on how stiff you want 3mm is usually too thin for local stiffness
Before you machine you need to look at thermal stress relief. After welding the frame will distort and then after machining it will distort again. TSR will remove the internal stress that does this so when you machine, the frame will stay put. The long members for the rails will need intermediate braces to limit deflection and to stop vibration. The twin gantry design is limiting in that the members are small and poor in torsion. Look at a large single gantry vs the twin design. Your Z axis plate needs to be thicker, the side flanges help but a thicker one is better especially if its high Z. Using light angle for the saddle to gantry car connection is a bit light on, either add webs to the angle or use solid blocks. These get twisted and bent a bit so the car attachments need to be very stiff
Its coming along - keep at it - Peter