Amon Ra is a permanent custom recovery, right? So it's too late either way, whether I use CWM or Amon Ra....
nope.not too late... you can flash the stock recovery back,just like you flashed clockwork or amon. i personally prefer Amon,always have. i havent been paying attention to wether the initial issues of clockwork have been worked out,but ive used Amon on along time on alot of devices,drellisdee,whom brought it to us,is a heck of a developer,and i have 100% confidence recomending folks use Amon. not bashing clockwork,but i do not have the same faith of it.
amon can be flashed permanently,or booted from fastboot when needed,as can clockwork(or any other recoveries that pop up for that matter

)
I don't feel like running custom ROM's. I might take the OTA, but before I do, I would of course re-lock, update, and re-root. I'm just tired of glitches in every aftermarket ROM I've ever run. Custom doesn't mean better. Frozen bloat is good enough for me these days.
the best thing for you then,would be to put the stock recovery back. if you keep the stock recovery you can just accept OTAs the wy they were meant to and not have to relock,run an RUU,and wipe out all your personal data.
sure,the OTA wipes out root. no biggie,just re-launch your recovery again after,and flash superuser again. bam! rooted OTA. one good thing about htcdev,is that you are unlocked,you can always reroot. gone are the days that you need to protect your root access cause an OTA may wipe out your exploit.
you can find the stock recovery here:
PH98IMG-2.01.605.11-vigor-recovery.zip
i would
fastboot flash recovery <recoveryname>.img it in place,and then if you need to go to recovery(amon or clockwork) simply boot it from fastboot with
fastboot boot <recoveryname>.img