So yesterday I spot welded the floorpans sections in the car. Next I'm going to clean, prep and POR-15 these new sections and the seams. Then from what I've read I should seal the seams using a seam sealer.

http://www.eastwood.com/ew-seam-sealer- ... black.html

When I was getting estimates on the floor pan work (which I ended up doing myself because they were $1500+) one guy mentioned he used the caulking that is used on the windshield seams. Would this be a good alternative?

I would use SEAM SEALER that is made for this type of application. I got mine in a tube to use with my calking gun. The window stuff may work but if you have to buy it anyways Id just get the right stuff.

I'm sure that the urethane windshield adhesive would work well. It is strong and flexible, just costs more. I actually covered the whole inside of my floor with a similar product. The Toyota Yaris had a recall where we covered the whole inside floor pan with what looks like thinner viscosity urethane to keep them from rusting from the inside out. We had some left when the recall was over, so I used it on my Spiders.
The 2 part seam sealers work much better for stuff you will see, the single art ones have a nasty habit of cracking.
http://autobodystore.net/Merchant2/merc ... _Code=JASS