It depends on what method you're going to use and how much your tubes are off by.
If you are going to use the stainless steel adhesive shim method with a long flat piece of metal, then you will also need to check the squareness to the other side so that your flat surfaces aren't canted to each other. If they are, you can do a small shim(s) on the outside edges of the longer shim(s) to make it square. With this method, I'd say you're looking at 1mm or so thickness, of course the thickness will vary and it depends on how warped the steel is. I have tried this with a wax based mold release and JB weld. Any normal epoxy should do, you can even mix in metal powder to the epoxy if you want.
If you're going to use the gravity setting epoxy (as opposed to squishing a thicker epoxy flat), then you need to buy the right stuff so that it will spread out evenly under it's own weight. I have not used this method.
The best example of that I have seen is in 1Jumper10's build thread:
http://www.cnczone.com/forums/cnc-wo...are-forum.html
Probably good for you to have a read through that thread, I think it will help you out with your build.
Like I said, the solid aluminum pieces I have are really flat, and it looks like your design bolts together. Perhaps go to your nearest metal merchant carrying a long straight edge with you, and see if you can find something the same size, but flat already. That would make things easier. The differences in thermal expansion between steel and aluminum could be a small issue, but personally, I would risk it. I'm not talking about T-Slot, But solid aluminum billet. Of course, measure the steel you have first to see where you are.
Honestly, I can't really tell what it is that the rails are sitting on from your CAD work. Is that steel tube or plate?
What province are you in, just out of Curiosity? I'm in Ontario.