Update for anyone following this thread:
First, our DS's early wakings got much better once his nose was totally clear -- I didn't realize how much just a little runny nose would affect his sleep, but it seems to have.
We're not totally settled into a solid single nap, but we currently set nap schedule by looking at wake time. If he's slept at least 11 hours, he seems to be able to tolerate 5.5/6 hours of wake time prior to nap. If it's less than that, he can't do much more than 5.5, and sometimes less. We put him down for first nap when he's tired, and leave him to sleep as long as he likes. If he sleeps long enough that we can make it to a reasonable bedtime (6:15-7:15), we shoot for a one nap day. If he wakes early or sleeps short, we'll offer a second nap. For the past couple weeks, he's done one nap for 5 days of the week, and the naps went from 1 hour 20 minutes, to 1.5.
What I've discovered is that for our LO, missing the window and keeping him up too long between sleeps is usually a recipe for early waking or short nap. I have to keep reminding myself this right now since we were able to vary his schedule more in the past (by that I mean that .5 hour didn't seem to make a difference, when right now, even 15 minutes seems like it can throw things off). Also, before the nap transition, he always seemed to catch himself up on sleep (by sleeping in or taking longer naps) whereas right now, we have to be careful to monitor how much sleep he's getting in a 24 hour period and be proactive about giving him enough time to sleep.
I hope this helps anyone who is going through similar changes. On the naps board and this one, there is a lot of information about the 2-1 transition that is really helpful. It's a tough transition for a lot of babies to begin with, and then if you throw in teething, sickness, and developmental changes, it can get really bumpy! Even though we still have our rough days, for us what's helped is just sticking to the plan above so that we don't second guess ourselves as much and hopefully, he'll get more comfortable in his new schedule soon.
HTH!