Well heres my take for optimal system performance and 8" run would be ideal. Will the 5" runs I cant say because I dont know what the supply plenum is and the return plenum . The key factory one would need to know is what ton system do you have now? Lets assume you have a 2 ton. If you go from a 2 ton to a 3 ton you wont have enough return. And may, lack supply flow. That would be determined by load calculations your home. So the return would need to be increase to handle the extra tonnage. And possible the supple feeds would need to go to 8". A 1000 bucks if you ask me is robbery, the stuff is cheap and its not rocket science to change it out.
If you ask me there all out of wack with there prices you should be around the 5K-6k mark. They all qualify for the tax break except the 13 seer unit but the furnace would. Anything 14seer or above, and the furnace depends on too many things, that they dont tell you. Best thing woudl be to check mfg web site to see if that furnace model qualifies.
Heres the thing when you increase the seer rating the cost factor goes up. Same would apply to the furnace, and require a new flue to be ran. So, again more cost factor and labor.
If I were you I would call 2 more companies. I know your looking at the tax break thing but your paying more for the equipment so the tax thing really is a wash for you, the end user. If it we me and I were you I would have the quote you the following: None of this qualifies for the tax credit
13Seer Condensing unit
80% AFUE 2 stage furnace (they can reuse existing flue, plus to this is it has low and high fire mode so it does not use near as much gas no special gizmos it does it on its own. )
Cased Coil (evaporator coil)
Line Set
Power Whip (fat wire from box below that feeds power wires to unit)
Disconnect Box (power box on outside of house)
Digital Thermostat (programmable or non programmable you pick)
Condensing Pad
They all come with a 10 year warranty and 20yr or lifetime on the heat exchanger. So, they bank roll the labor thing into the price to cover there behind, should a major component fail IE the compressor. So toss out the labor thing and knock off somewhere from 400-600 bucks.
I think you'll be shocked as the numbers you get back it should shave a good 3K off what your getting quoted from the 8K number. Where im at they sell all day long for about 5500 or less with what I suggesting. If you going for the high efficiency stuff it will take you 20 years to get your investment back, not to mention with the higher efficiency unit and furnace when they are out of warranty they are expensive to repair. So, you have to ask youself how long are you going to be in this house?
The reason most dont go in the attic if the furnace is not in there the generally tend not to go up there. And no offense some of these salesmen they send out cant even turn a screw driver. Its all preset pricing. So, they go, look whip out a price based on what you have bingo bango. Then try and up sell you on 4 inch filter media, electronic air cleaners, UV lights, a programmable thermostat that could run the space shuttle, ect.
Try and find a smaller company that gives the personal attention to detail, and explains every thing. If they listen to what your needs are and there not out to give you a one over. I guess I;ve run into this way to much over the years, where the homeowners is so freekin confused they don;t know what too do or what to choose. Sure is the high efficiency stuff nice, but I always have to look at it from there perspective and what make sense. To say as just to make a quick buck.
Lastly the correct way to go what ever seer rating you get or furnace is to have the parts that I listed replaced.If the equipment is install correctly you should see many years of trouble free service.
Lastly, I would suggest, if you exclude the labor warranty, use the money for a Preventative maintenance program . That the real key to equipment longevity. Plus make sure you change the furnace filter at least 4 times a year and use a good pleated filter. Not the mesh style ones that are 3 bucks. Hope this helps for some food for thought. Good luck !