I used 12 1/2mm round rail and mdf for the build and because of this the machine is weak? Fragile? I don’t know what the best description is.
What are you using for the spindle motor? If you intend to use anything heavier than a Dremel, then you really need to consider using larger diameter rails. The flexing in a 1/2" (12.7mm) rail is too great for anything other than cutting polystyrene; seriously. Nick at RockCliff stresses that in his forums that his initial designs used 1/2" and he has since up graded to 5/8" or 16mm. It is amazing how much more rigidity that extra 3mm provides.
As for MDF -- if you used the 19mm as spec'ed, you will have ample strength for cutting even light gauge metal sheet.

I have been using a B&Q 1020W £20 router with a modified base -- it is heavy at 2kg, and with the Z motor at 1.85 Nm I can't drive it quicker than 300 mm/min or it stalls out. I'm using motor driver modules from http://www.jafmotion.co.uk/motordrives.htm that I think need to be used with caution.

The other thing to ask is do you need backlash compensation?
To prove it maybe cut a square with your 3mm cutter and repeat it many times. If the track is still only 3mm after 10 or 15 repeats, then you do not need backlash compensation.

I need to get a new X/Z interface plate made in Al with bearing blocks in Al that won't shake loose in time.

My machine was built using 19mm MDF as per the plans; 16mm and 5/8" guide rails (redeemed from plotters and ebay), and Oil-Lite sleeve bearings; Lead screw 10 x 1.5 mm standard threaded bar from B&Q. FL57STH76-2808B motors from http://www.motioncontrolproducts.com/nema23.html.

cheers