All Done
Well I got the new parts on there, I was going to take pics but after I got into the job I realized that it was so easy and self-explanatory that pictures weren't necessary. I didn't remove the door panel or the mirror, all I did was roll down the window and pull up on the plastic piece at the end toward the door handle (the plastic piece is the part that looks orange and almost white in the pics because it is so badly oxidized). If yours is too badly rusted at the end you may have to pull the rusted end out and then pull up from the middle where the metal underneath is solid, either way it should come out fairly easily.
I then cleaned and waxed the paint underneath where the strip sits before I put the new strip in. I also applied a coat of thick oil to the underside of the new strip, the clips, and the ends of the strip to prevent it from the same fate as the stock ones. You'll be able to see where the rust starts by comparing the old strip and the new one, the ends of the strip are bare metal from where the sheet metal was cut at the factory. If you use oil or grease, be careful not to get it on the felt that sit against the window, otherwise you'll have a greasy window every time you roll it down.
Once you have the new strip prepped to your satisfaction just slip it into place starting with the end toward the mirror because it sits slightly under the mirror, with a little bit of careful maneuvering, the new strip will slide right in.
Finally, theres the problem of where to buy the strip. I bought mine from partsguyed.com because they had the best price and it was a genuine motorcraft replacement part, which I thought was impressive. It can be found at this link
Partsguyed.com
The strip is part number 5 in the diagram, this link is for 1998 and half of 1999 but they carry the part for other years as well.
It can also be found at LMC truck as mentioned earlier, the link for that is here
LMCTruck
It is part #29 in this diagram.
Finally the part can also be found at Fordpartsdirect, which can refer you to a local dealership if any of them have it in stock. Their prices are only a few dollars more than the others, but if you can find it at a dealer it may be cheaper and there will be no wait on shipping The link for that is below
Ford Parts Direct
It is part #21452 and 21453.
I hope this is helpful to someone else, and thanks again for your help.