If you are competent at sewing a zip, then I don't see any real problem. I'd probably remove any seam seal tape (warm iron and brown paper; the reverse of my OM article on repairing waterproofs). Then open up the seam and insert the zip. You shouldn't need the extra fabric provided by the seam allowance to insert the zip, but it's always nice to have a bit of spare to play with...
I'd probably insert a placket on the upper half to protect the zip from rain; any old waterproof fabric that's to hand, folded double. Sew the placket between the outer and the zip. Probably easiest to sew the placket to one side of the zip (on the outside face of the zip...) before inserting the zip as normal.
Then tape the zip seams. There will be a small water path to the zip backer fabric via the threads of the seam, but you can always run some DWR treatment along it to help.