In principle epoxy levelling is worth-while on both the X (longest) and Y (across gantry) axes otherwise you are only getting some of the advantages.

In your case the Y axis will be difficult unless perhaps you epoxy the top rail, then when dry and the rail is fixed turn it upside down and use a DTI to dial in the other rail whilst it has a fast setting compound under it? I've not used them myself but I think Dean has talked about some kind of putty instead of shimming?

For the Z axis epoxy is not required as you would ideally use Aluminium EcoCast plate which should be pretty flat to start with. Alternatively you can use standard aluminium plate and skim it flat on a milling machine as the part is quite small.

With the welding MIG is nicer to use, but should be OK with stick/ARC for what you are doing.