So after importing syncing audio separately into Final Cut Pro X then exporting to Vimeo, listening on stereo devices or speakers sounds great. Mono, however (MacBook, iPhone, etc) sounds terrible. Audio is flat and barely has any volume. I've had to fix it by what feels like a poor-man's version and change it to dual mono then mute one of the channels.
I'm recording separately on a Zoom H4N using an external shotgun mic. Am I missing any settings when I record, or is it a specific setting that needs to be changed in FCPX?
This sounds like your 2 tracks are out of phase with each other. That leads to major cancellation especially in the lower frequencies. I don't remember if there's a way to reverse phase in Soundtrack Pro or FCP. Consoles and many audio plugins have phase reversal switches. If you can't find that, and need more gain, copy one of the tracks and paste it back into the sequence. If it works with just the one track, you're good to go. This is why mic placement is so critical. Read this article about the Rule of 3s and phase cancellation if you want a more detailed explanation.
MacPro 8-core 2.8GHz, 16 GB RAM, OS 10.8.4, QT10.1, Kona 3, Dual Cinema 23, ATI Radeon HD 5870, 24" TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 3 (FCP 7.0.3, Motion 4.0.3, Comp 3.5.3, DVDSP 4.2.2, Color 1.5.3)
FCP-X 10.0.9, Motion 5.0.7, Compressor 4.0.7
Pro Tools HD 10 w SYNC IO & 192 Digital I/O, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec DSP Monitors, Prima CDQ120 ISDN