This may seem like a stupid question, but I've finally finished the main quest, at level +70. I went to all the different dragon roosts across skyrim, killed them, and then waited a total of 41 days inside breezehome.. They still have not spawned.

They always spawned before I finished the main quest.. So... Anyone else have a similar experience?

Is this just after the Patch?

I haven't had this happen. Went to Shearpoint and got the word, then came back a few days later to test Lydia's mettle against an Elder Dragon. Elder Dragon was there chilling on the wall.

Yeah, in my game, those dragons respawn, but I can't re-absorb their souls ...

I've never had dragons respawn anywhere, I have met different dragons at word walls after I'd been there... like maybe they're attracted to them or they figure we might be. I also had something in the neighborhood of 10 total dragons attack the stables at Windhelm. If I learned a new word and didn't have any souls for it, I'd fast travel there and WOOT... had a new one. It was sick. Cool, and sick. Those poor horses are either the most abused or toughest horses in my game.

dragons don't end as long as we're in the game unless part of the rebuilding quest with the blades is to hunt them into extinction again... I wouldn't know yet.

you can keep them from showing up in the first place by not doing the quest for Whiterun... for instance I've just started seeing dragons on my newest character now at level 26 because she had to pick up the quest from Balgruuf/Farengar in order to advance the radiant quest for the Thieves' guild in Whiterun... (do you KNOW how irritatingly capable of finding you Irileth can be when Farengar is asking your invisible self "and who might this be?" following you? argh... it was just easier to go ahead and say I'd get the stone for them.) I went ahead and did the kill the dragon part because it seems just silly to carry it around after waiting so long to start it.

Yes they do continue presumably forever...

I had the same thing happen to me with the plethors of dragons all about, except it happened to me near the hot springs...I just ran until they were no longer near me...It was crazy, I couldn't do anything about it but run, just like the Dovakhin in the Skyrim trailer...I hauled a$$...