Hello and welcome Xavi,

Ok well straight away can tell you that you need to considerably beef up the gantry and use better design. As you have it now it will be rubbish for anything but plasma machine.
It's A weak and poor design with not very good balance regards Centre of Gravity (COG) and cutting forces. (Don't under estimatemate the FORCE luke.!!)
Will need to be much much stronger with more rails and bearings.

The base frame is resonable but like Matt suggests some more support and triangles will help.
However the idea of using Angle plate to attach rails is bad idea and will be harder to make work than bolting directly to the steel. The type of linear rail your thinking to use isn't very tolerant of uneven surfaces and angle isn't very flat unless machined flat.
Also with having the rails on there sides you have the problem of making sure both sides are perfectly parallel and on the same plane in both vertical and horizontal, or if on differant planes both planes are exactly parallel to each other.
This is why you'll often see rails on flat surfaces which each side can be brought onto the same horizontal plane much easier and setting the rails parallel to each other easier.
The way you have it Sooooo much harder to do without machining reference edges etc or some way to align etc.

Don't get too hung up on protecting the rails because they take an awful lot of abuse and crap before they wear out and there are easy ways to help protect if required.
If you want the rails lower than the surface then simple attach another piece of box section on the frame sides but lower down and sit the rails on those. The Rack can then go on the under side so protected from Crap which is more important than protecting the rails. If unsure what I mean say so and i'll knock a sketch up.
Doing this will make setting the rails on the same plane etc much easier either via shimming or using something like the Epoxy method.

I suggest you have a little look around at other builds and take notes on Gantry design and Z axis. Doesn't need to built like tank from armoured steel plate like some you will see but does need to be strong with good design. Esp the Z axis which takes all the cutting forces.

Hope this helps for now and don't let mine or any other negative comments which will probably come put you off. We are just passing on experience and you will thank us for it if see it thru to end.!!