David,
In response to your question, "yes, it's just you". We started a couple of months before you, and everything in our office runs as smooth as silk; on autopilot. How about this: send me a plane ticket to Fairbanks, arrange a couple weeks of camping, hiking, and boat tours, and I will spend a couple of hours in your office getting you up to speed...
We are right with you. I think the big "unspoken secret" about transitioning to an electronic record is the fact that the EMR program itself is only a small part of the process. Yes, it is essential to have an intuitive, functional program, and I believe that AC fits the bill (at least for us). But in reality, that is just one of a number of issues to address. Next you have a series of concerns related to IT (e.g. networking), security, document management (faxing, scanning...the whole "going paperless" thing), intra- and extra-office communication (messaging, emails, letters), and on and on. All of those issues must be addressed as you try to learn how to use the program.
What I am learning (sometimes the hard way) is that implementing an EMR really involves completely re-examining and re-imagining the work processes in the practice. In a sense, you need to re-think every little step of every staff member's job. You can try to change as little as possible, but in fact what worked before is not likely to be what works best going forward. I am fortunate to have in-house (in fact, "in family") support and management for this, otherwise I think I would be pretty overwhelmed by the process. I expect the adjustments to continue for a few more months. In a sense, though, this will be an ongoing process that goes on forever....unless I get all my answers at the ACUC.