What I did and recommend you do is to replace it all with one unified unit. A single unit will be much easier to do maintenance on and less costly in the long run. It sounds as if you will need to have some duct work done too but it should be worth the time and money in the long run. It also sounds from your description that one unit serves both far ends og the home so the majority of duct work that is likely to need to be done is just joining it all together. The size of your home is pretty small. My ranch is about 1723 sq. feet. I have a 3ton heat pump with a "dual fuel" kit utilizing the gas furnace as back-up or emergency heat rather than the expensive electric resistance heat typically used in the past with a heat pump system. My local utility company offers energy audits in which they will come out and audit your home. They offered several ideas on areas that I could improve the energy efficiency of my home. The good part about this was that they also offered grants or incentives to do the work too! My heat pump system cost about $700 more to install that a separate a/c and gas furnace system but my utility company paid me $550 for having the work done. I got $550 to insulate my attic. It cost me $400 to do have it done so I made a little bit. The crawl space needed more insulation too. They paid $250 for that. All in all the extra expense I incurred in my install was offset by the audit and grant money. Call your local utility (GAS too!) and see what they'll do.