Just before i read your last paragraph i was about to suggest switching to one nap. Somewhere in the middle of all this turmoil, he might have grown enough and just get ready to that. Specially if the long time settling is jsut for naps and he's ok going down at night. For what is worth, i think you've done a great damage control, cause you've been able to provide him the environment and routines needed to get a good sleep. And all the diseases and teething have threathened your sleep training but you've done such a consistant and great job!!!!!
Now, if you're feeling it's time to switch to one nap (i have that feeling too), i would recommend you to slowly increase his awake time, and see how much Andy can hold without getting overtired. Try with 15 mins increments of awake time before each nap and if he does fine, you can even try 30 or 45 mins. Try to offer him a snack at the time he would usually start getting ready to go down. That should provide him enough energy to hold on for longer awake time periods and hopefully push the schedule in a way that the second nap will vanish till it dissapears. Meantime, don't fight naps, especially the second one. Try this to gradually become a catnap, be it at the stroller, car, etc trying that he goes down easily and for shorter periods.
Let me know how you get on and if you have any comments/doubts/thoughts on this. CONGRATULATIONS again for your hard work! i promise you're just about to turn a corner, with all the molars out and a great sleep training process on its way to finish! HANG ON!!!!!!!