I had one of those radios for a few months. It's been a few years, but I only used a 949E at the time.
If I was in your situation, I would use the 949 exclusively. I believe you can quickly bypass the FC-30 can't you? If so, I suppose you could put the 949 after the FC-30 and and switch it to bypass mode while your using the FC-30. When you want to use your 40/80 meter wire, just quickly push the tune button to bypass the FC-30 and select which antenna port your going to use on the 949 and load the wire up on the MFJ.
This is only if you can quickly bypass the FC-30. I believe you can, but I'm not sure.
Anyways, I'd dump the FC-30 and use the MFJ. Maybe you could sell it and raise funds for a good LDG or MFJ autotuner. I use the MFJ-929. It works really well and tunes a wider range than any LDG.