When doing a body restoration it can be a good idea to fill some 'blind' area with expanding gap-filler foam as obtainable from Home-Base and other DIY outlets.
The places worth doing include;
The enclosed areas at each end of the screen scuttle panel which can be accessed at the inner rear ends of each wing.
The ends of the rear valence, after drilling some holes at the bottom edge to let the foam out as it expands.
Around the jacking point by way of holes drilled in the inner sills.
It may be worth considering doing the bottoms of the rear side companion boxes beneath the liners to keep the rear quarter panels from corroding.
On a Mk.1 & 2 I've seen foam added at the lower screen level into the A-post void where it meets the A-panel and front wing. Sometimes there is a small gap around that area where water can get in from front wheel spray, but be careful in case the foam expands and pushes the outer panel surface outwards. I remember a friend who filled the new sills on his Triumph 2000 with this foam and he didn't put enough expansion holes in. It split the new sills from the body-shell!
Allow sufficient expansion holes, trim off the foam which projects from these holes after the foam sets and use a little bit of body filler to seal the holes off then paint over them with body colour.
Any way of keeping moisture out is good on a classic Mini. In fact I've just done one side of the '64 car I'm restoring.