Yes this house is pretty strange. Its an old farmhouse and when they put in the oil furnace (which we don't use) they just sort of slapped the registers here and there. We basically just stopped the cold air with batting and sealed it up with duck tape (neon pink). its already made quite a difference.

It would appear that somehow your fireplace insert is tied in with you regular heating system. You will have to go do a little crawling around and tracing of the duct work and block it off where it needs to be. You have to be careful though to make sure it doesn't affect the rest of your system. If you're not comfortable doing it or not sure you're probably better off hiring someone who will understand what they're looking at in your house. It's pretty difficult to see into your basement from here.

It sounds like your home had floor furnaces at one point. The large return air grilles sound like old openings for floor furnaces, used a long time ago. Where to start? First, your system should have filters somewhere in the return duct or inside the air handler or furnace. I would look really good to make sure you haven't missed something. I've seen filters placed in really weird places. Sometimes filters aren't found for years. By then they're pretty stopped up. As far as the return grilles being large, the larger the better! One thing that kills your system and your energy efficiency is duct work that's just too small. Modern systems are made to run with very little static pressure in the ducts, around 1/2 inch. That's not much, so I wouldn't worry about the large ducts. The filters are another story. You really need a filter in your return duct somewhere. If there's not one, i would install filtration. Usually the cheapy filters work best as they cause the smallest pressure drop in the duct. You mentioned the refrigerant leaking out. If you have a refrigerant leak it should be repaired. That stuff ain't cheap. Besides it's illegal for a technician to keep adding without repairing the leak. If someone is having to add refrigerant, you definitely have a leak, no question about it. If the service provider you called did not look at your duct work, did not tell you your system had a leak, and did not offer sound recommendations, please ditch them and find someone qualified. As far as your system coming on and off every ten minutes or so, that's called "short cycling" and isn't good for your system, your energy costs, or your comfort. It sounds almost like your system is either too large for your home or you have massive air infiltration. Either way, this needs to be addressed. Really, I would recommend you find a good service provider in your area that can be trusted to offer technically correct advice. I usually find it best to ask friends, co-workers, or other family who they use and trust. In the meantime, you may want to check out a couple of articles I've written dealing with heat loads and your comfort. Here's one HERE if you would like to read it. Let me know if there are specific things I can help with. I'll be happy to help if possible.

What Hallett & CO suggested, that's the place to go. Ordered a few custom grills from there, they do make nice stuff. Just make sure you specify Material-Steel Design-Metal and that it will be used a floor return grill.