New Home Owner Needs Help

My air conditioning system went out during a storm and got cooked by a lighting strike per a service tech. I have had multiple people look at my system (a 3 ton split per everybody). I've narrowed my choice between 2 companies, one wants to put in a Trane 90 plus furnace with a 14 seer ac unit but I would have to repair holes they need to make to run some piping outside. Another wants to put in a Carrier Infinity 80 percent variable speed with a 15 Seer Infinity ac unit and Infinity controls. There is not much of a difference in price. The Carrier guy said we never use the furnace long enough to get a return to justify going to a 90 plus furnance. Isn't 90 better? But the Carrier rep said I need to do some more work that nobody has said. I had a home improvement company replace my water heater recently. The Carrier guy said they did it wrong and it should be changed out prior to him starting work because he pulls a permit. He said the water heater should have been a "tall" style placed on a stand with a drain pan and drain connected to something. The one installed is 28" round and almost touches the current furnace. I had to remove the door frame for them to install it. He also said that you need to be able to remove the unit without removing any construction. He said you have to be able to reach parts to service it, the "drain" at the bottom hits the door frame. And something about sharing combustion air between the two units. He also said since they are both in a "mechanical" closet there should have been a louvered door for combustion air (the current door is solid). He said my inspector should have caught that when I bought the house from the previous owner. He also said there should have been a "why" connection at the water heater and furnace. Is there a clearance requirement between the water heater and furnace? Is he just full of baloney or what? Which would you go with, I live in mero Atlanta? I need some good advice.