If this were my choice and my money, based on my experience, I'd go with the 13 SEER 410A system, standard fan and the contractor I trusted. If it is a heat pump system and the 3-ton was sized right at the limits of the load calculation, I'd go 3.5 tons. The southern summers are not getting any cooler or less humid. Plus your old house does not have a tight envelope and on those 100+ degree days that additional 1/2 ton of capacity will be nice, as will the additional heating capacity in the winter.
One thing you will get with HVAC guys is a variety of opinions. My philosophy of HVAC and life is to not complicate things any more than necessary. Keep it simple. The 13 SEER will cool and heat your home just as good as the higher SEER units and you can save the $1,500 to put toward new insulation, windows and doors, which will save you a lot more in the long run than will the more expensive units. The repair parts tend to be more expensive on the higher SEER units as well. It is considerably cheaper to replace a standard fan motor than a variable speed motor, and the standard motor is usually generic, whereas the variable speed motors are most often proprietary and consequently even more expensive, especially Lennox, Carrier and Trane.
Buy the 13 SEER 410A unit from the contractor you trust and be happy!
As to running the fan 24/7 - I do not do this because it wastes energy and does not make me any more comfortable than cycling the fan, plus it wears out yout motor bearings sooner. Some people like to run their fans constantly, and that works for them and makes them happy. Do what makes you comfortable.