The first cheapest "fix" is to get a cover for the cowl vents. These are available from all Mustang places and basically keep the water out of the cowl area. Does not fix the problem.
The next is the plastic hat replacement. I tried this but had rust thru the cowl pan that I couldn't get sealed working under the dash.
Third fix is to pull the fenders and make slash cuts at the end of the cap so you can reach in and slobber sealer all over the cowl pan. (check out
http://home.pacifier.com/~dnstoys/mustang.htm )
Finally to do the job "right" requires removing the cowl cap. This starts with pulling the windshield, hood and fenders. Then cut the 140 to 170 spot welds to remove the cowl cap. You can then examine the cowl and decide on a fix. Either replacement or give it the corvette treatment (use fiberglass to rebuild the cap, this was my choice). Once you have the cap repaired, sealed and painted, you should be able to hire a welder with a portable set up to plug weld the cover back on. The site above has a link to a page that shows the complete repair.
You definitely want to do something before the floor pans go. (Suggest you pull your carpets to check the current condition of the floor pans.)
Good luck.
[This message has been edited by John Z (edited 09-07-2000).]