Todd: The restoration of 356 cars has a cult following and that cult usually (but not always) has very deep pockets. A friend of mine bought a pre-A coupe semi-basket case that I would have walked away from (and my metal-working skills are pretty good). He was a neuro-surgeon and really, really, really wanted this car. He had it transported to Meister Restorations in New Hampshire and there, after almost a three-year process, took delivery of his restored dream. Meister did a superb job - the car absolutely looks brand new, inside and out and is a gorgeous Bali Blue. He bought the car for around $60K and dumped another $120K into it (all he'll own up to) and still figures he came out ahead. He also drove it to the Porsche East Coast Holiday this year (in Georgia? I think) - Had 150 pounds of spare parts with him (he's still building his mechanic skills after retiring from Veterinary Medicine) and never used even one.
Given all that, I would still expect the car to return to Meister every other year (if not sooner) for touch-up work as it is still a metal car and will still rust, somewhere, starting with the Battery box.
If you get the floor and sill metal and do the work yourself, I would expect the cost to be several thousand, at most, assuming you can remove the spot welds (there is a special hole saw for this) and weld in the new panels yourself. Be aware that you'll probably end up buying $200 - $500 worth of tools to do the job, but you get to keep those as an investment. The new panels won't be spot-welded as the originals were (lowering its' future resale value) but it will be strong and last, especially if you weld all along the panel perimeters. Remember that as you begin to remove the obviously rotted metal in there now, you will assuredly find even more rotted stuff lurking behind the obvious stuff - It just goes on and on.
If you take it to some place like Meister Restorations in New Hampshire (and there are others around the US), plan on a 1 - 2 year queue and then another year for the work to be done and somewhere in the vicinity of $20K - $30K unless they find more things to fix while they're in there.