First of all something is wrong with your heat cycles. The furnace should be off for at least 10 minutes or longer not 6-10. A 110 WAV I would replace with a stage 70,000 EL296V but not go to 45,000 and I do not believe anyone makes a 2 stage 45.000, 60,000 is probably the smallest in a brand I do not like. If you can get the cycles/hour down pat it should work a lot better, being oversized nothing I can do about it but it won't really shorten the life of the furnace. Contractors oversize furnaces because some of the salespeople are idiots and to be on the safe side they tend to go with a larger size so that if they undersize they won't be stuck removing it for free. The tstat may also be getting a draft thru the wall behind it so they should remove it and stuff the hole with fibreglass pink insulation. Drafts will definetly short cycle it and there should be no return air grills within 6 feet of it or that draft if you run the fan all the time can affect it. Do you run the fan all the time? I would with the V drive and it will make your house more comfy. I checked the install manual and there is no cycles/hr setting but the differential between 1 and 2nd stage can be set for 1-3 degF so a 1.5 -2 may be better. Need to get the installer to go into the setup menu to do that. I would get him to check the hole/draft behind it first and then increase the differential to give longer low fire and better comfort. Better yet get the proper sized furnace but that is another story. The bigger companies have comfort satisfaction guarantees or they will remove it so if all fails try that.