Just for anybody who is looking for info.

Boot was water leaking in via the seams around the boot hinge, that square box the hinge is in. Also sealed up all the seams in the area just in case.

Water in the footwell was due to cracks in the bulkhead seams, about 2" below the windscreen. Done from inside the car, glove box out, all the old material chiselled out then re-sealed. Sorted on the 3rd attempt.