I now have a new problem, Armory is reporting that it is online and connected, but that my balance is 0, which I know it is not. After opening bitcoin core, it says it is catching up, that it is 40 weeks behind in importing blocks from disk. Could this be caused by armory downloading the bootstrap but bitcoind not having fully integrated it yet? Once bitcoind catches up, will I need to rescan, rebuild and rescan, or redownload the entire blockchain from armory? I'm thinking that I will just need to rescan, or that I might not even have to, that once bitcoind gets up to the point I received my coins that it will show up in Armory.
Could use help.
Are your coins in a Bitcoin Qt wallet, or an Armory wallet? (you're right about your last point BTW, the blockchain downloads more or less in order, so if you're missing 40 weeks and you sent coins less than 40 weeks ago...)