Assembling & alignment precision concerns

[JAZZCNC]

Ok well your thinking is sound and milling a Reference edge is correct way. Regards aligning the other rail then it's not has difficult has you may be thinking.! The correct or official way will use all kinds of precision measuring equipment but the way I'm going to explain works just has good just takes longer.

Simply mount first Master rail to ref edge and bolt securely then align opposite rail parallel the best you can either by very close measuring or using gauge block. (I actually have a long bar with locking slides that locate into counter bores of rails mainly to speed process up a bit.)
Don't fasten this rail down fully just nip up enough so it can slide but not lose and sloppy.
Now fasten the Master rail bearings to attaching plate and same again only tighten opposite bearings so they can slip.
From here it's mostly feeling your way.!!
Put bearings on rails and run up and down rails to align bearings then tighten bearings down evenly. Chances are you won't feel any tightening of the bearings on rails but check they haven't locked up.? If so then chances are your plates are twisted or not flat.

Now it's a case of running the assembly up and down the rail and tightening the rail bolts feeling for tight spots or any binding at same time. If you feel any binding then quick nudge of the rail in either direction will bring into line. If the bearings lock while tightening rail then it could be mounting surface isn't flat and you may need to use shims.
When I say shims then I'm talking very thin shims, like paper thin or less, can often make huge difference and remove it completely.

That's all there is to it really just careful alignment and feeling your way.

One other thing is that I see you mention SBR.? If that's the supported linear round rail then most of this will be irrelevant because the precision of them is not that great. Here I'm mainly referring to Profiled linear rails.
With Round rail then the tolerances are far lower so they don't bind easily unless drastic out or fastened to bent/twisted plates and has such take much less to align. Down side is they are not that accurate.!!

Being totally honest you won't get the tolerance's your speaking of from Supported linear round rail. The procedure is prity much the same just far less critical.