Replacing carpet and top, but I've caught the "While I'm in there" bug!

I am so glad that Dev brought up the under-carpet jute pad.

IMHO, the reason for the rust on the floor pan, and the funky smell/allergic reactions while riding in some Spyders is due to the jute under-carpet pad.

Shortly after I bought my, poorly maintained Spyder, Itsy-Bitsy, I decided that I could not stand to smell the scents of cigarette smoke and mold/mildew even another day. So I pulled everything off of the carpet and then pulled the carpet up as well. What I found: the carpet ---- and therefore the carpet pad as well ---- had been wet multiple times (snow/slush on shoes, partially/full open windows, top down in rain, etc.) over its 17 year life span. In fact, in several places under the seats, the jute carpet pad was still water soaked when I removed it! 

The problems with the jute glued under the carpet are: it appears NOT TO BE water resistant and absolutely is NOT WATER PROOF; as a natural fiber, once wet, jute ---- at least in the case of my Spyder ---- seems to be one of the more productive media for growing molds and mildews.  Lastly, because the floor drain holes in the Spyder are completely sealed --- as opposed to having one-way valves to allow water to leave the Spyder's floor pan --- with rubber grommets, once water leaks through the carpet, soaks the under-carpet jute, it lays on the bottom of the Spyder's metal floor pan --- supporting mold/mildew growth in the jute --- until such time as it evaporates (very, very, slowly) in reverse order through the carpeting and then through the under-carpet jute.

IMHO, ideally the Spyder's carpeting should be backed by a mold/mildew, water proof, high density closed foam.  Also, ideally, at least some of the Spyder's floor pan drain holes would actually have one-way valves to allow trapped water, which drained through the carpeting and/or closed cell foam to quickly exit the vehicle.

So, in addition to fixing very, very minor rust damage, I installed Dynamat sound proofing.  My plan is to remove absolutely as much of the jute backing off of my new (+$450) new carpet and then to use Therm-a-RestRidgeRest SOLite Sleeping Pads as carpet pads.  I am experimenting with the SOLite pads because I like the idea of the pads molded design trapping dead air thereby increasing insulation value.  The pads aluminized surface reflects heat and, the pads seem to be fairly water resistant. Because the SOLite pads are made of polyethylene foam, they should also not encourage the growth of molds/mildews.

The only major drawback I can see with using the SOLite pads under the Spyder's carpeting is that folks entering and exiting the vehicle will surely be able to feel the "Give" of the pad.  Whether or not folks perceive the "Give" to be a "Plush" or a "Squishy" sensation is yet to be determined.

Once I actually have the SOLite padding installed and in use for awhile, I will add my feedback to this post.

Any/All suggestions for replacing the under-carpet jute pad with an alternate water/mold/mildew proof padding would be appreciated!

You need to be very careful not to create a "moisture sandwich". I carry this concern over from my earlier days as an amateur tilesetter/shower rebuilder.

The jute, while nasty, does eventually dry out. While you might think that drain holes will be the answer, water is capricious, has a will of its own (capillary action will thwart your drains), and generally likes to cause trouble.

I am not offering a detailed solution, just a word of caution. I think you are on the right track by elimination all of the mold food, but the water needs somewhere to go, and it will not submit to gravity as readily as you would hope.