If it was me I would stick to a set bedtime as well as naptime for a week and see how you go.
If, as you say early bedtimes lead to early mornings, does putting him to bed early help? If he's up at 6.30 do maybe 12pm or 12.30 for a nap then 6.30 or 7pm bedtime. If he's going to NW anyway maybe get his bodyclock used to that daytime routine for a while.
I know what you mean about a BW'd kid - it's not what you expect/hope for - but maybe you just hit a growth spurt, a developmental spurt, teething and illness all in a oner (who knows?!) and that has completely thrown him and his internal rhythms. So maybe now is the time to set a new routine and just stick to it. It'll be no time before he may not even be wanting a nap anymore anyway so you may as well just find a routine and stick with it so at least both of you know where you stand (although that is maybe a little un-BW!).
You are reading cues, which I never really mastered, so fair play to you for that but I wonder if they get to an age where you just need to choose a routine and stay with it until they get with the program!!! Just set his routine (naptime and bedtime) and then work on extending his naps if you think he needs that. When I went to a set naptime, I couldn't change his bedtime around as his older sibling (3.5yrs) has the same bedtime and there was no way I could juggle dinner/bathtimes/bedtimes to stagger bedtimes and he just got used to it.
As for his naps, does he go nuts when he wakes for his nap? Have you tried WI/Wo to extend it recently? Are you able to leave him there to at least continue to rest when he wakes?