This all sort of goes in a circle so here we go....
If you want more strength in the mini body start with seam welding the subframes, seeing as the front subframe will be heavily modified your probably only going to be left with the suspension towers and rear webbing section but they are the main sections to seam weld anyway. The rear sub frame can be welded or if your in a modifying mood and know a good engineer throw the std rear sub frame in the back of your shed and get, make or mod a std sub frame into a "rear beam axle". Save weight and gives more room under the rear of the car and it opens up the area for your rear coil over mods.
Now with the rear coil overs you have to cut out the original shock absorber towers and replace them with larger diameter tube sections that fit around the coil overs, just remember to do this with the rear trailing arms near by so you can double check you have clearance around the coil over at full suspension compression and fully unloaded. New tops on the suspension towers/shock towers (they are now the same thing) need to be made and seeing as these new towers will hold all the weight and force of the rear half of the car it all has to be made out of decent steel not just 2 1/2" exhaust tubing
. Once the new towers are fitted a brace bar between the tops of the towers wouldn't hurt for more strength, but that means you can not use a std mini fuel tank.....but seeing as you (may) now have a rear beam axle you can use some of that extra space to add a new alloy drop tank in the boot floor.
Now seeing as you want a roll cage you could go for a six point cage and tie that into the rear suspension towers which will provide a huge heap of rigidity joining the rear suspension loads to the entire floor pan, B and A pillars and the fire wall (the car now is basically a space frame body now) and this will also delete the rear seat, weather or not you can legally run with out a rear seat "firewall" section (I'm talking about the rear parcel shelf and rear seat back).
And now with the six point cage were back to the front of the car where the cage could be extended through the firewall and join up with the new front subframe which would have to be built with this in mind.
It all depends on what you want the car to look like in the end, if you want mad body strength you'll have to go with a space frame race car inspired build but if you want it to look like a normal road car you'll have to forget about a six point roll cage and therefore a super strong and ridged body.