That's a hell of a lot of stuff in one ask..! I'll see what I can do.
Not on AO3
Given that you've read the Resurrection-verse you may have found this already, but Elspethdixon and Seanchai have a fic currently only held on LJ, which hits a lot of your buttons (Tony whump/people being BAMFs/Steve/Tony pairing):
When The Lights Go On Again (http://cap-ironman.livejournal.com/177544.html) (LONG, 616-verse splitting off from late 90s canon) Aliens have invaded earth, and the Avengers are scattered. While Steve leads the resistance, Tony once again finds himself playing captive scientist. In the midst of a violent alien regime, separated by seemingly insurmountable boundaries, Steve and Tony have nothing to keep themselves going but each other.
Valtyr also has a non-AO3 fic: Conjugate (http://kijikun.slashcity.com/Conjugate.htm) (Medium-length, 616-verse from around the start of New Avengers) The New Avengers get their powers switched around. Peter sniffs people. Steve sticks to things. Logan lies around and drinks beer. In a surprising twist, Steve and Tony make out
Brain-delete
Have you read Without Irony (http://archiveofourown.org/works/148868) by tsukinofaerii? (58k words over 2 fics) Sometimes, when a drive is completely broken, the only thing to do is wipe it clean and start over
Other things set during this period:
The beginning is always today (http://archiveofourown.org/works/817306) by marinarusalka (18k words) After the siege of Asgard and the defeat of Norman Osborn, Steve is busy with his new duties and Tony is busy establishing Stark Resilient and working on the new Iron Man armor -- until Tony is accused of murder. Now Steve and Tony must work together to clear Tony's name. If only they can stop arguing for five minutes.
Sea Stars (http://archiveofourown.org/works/9945) by Muccamukk (42k words) Steve comes back to life somewhere entirely unexpected; Tony doesn't remember being a hero; something is rotten in the province of British Columbia, and the 2010 Olympics are doomed.
This one is set a little later, but I'm recommending it on the basis that it's got plot, porn, whump and BAMFery: America Isn't Chicken (http://archiveofourown.org/works/860801) by Amuly (130k words) After a Civil War, death, rebirth, a takeover by Osborn, brain deletion, and the fall of Asgard, Steve and Tony might just be starting to get back on solid ground with one another. Things aren't perfect, not yet, but they can be in the same room as each other without resorting to violence, and they've even managed to share a smile or two. Seems like the perfect time, then, for Tony to try and fuck it all up with a stupid game of gay chicken.
time travel/time loops
I have over a dozen fics on my list containing some form of time-related shenanigans, so I'm not going to list them all, but I assume you've read The Twice-Told Tale (http://archiveofourown.org/works/411599), which is the closest match to what you want (MCU)?
There's also:
And Has Time Enough (http://archiveofourown.org/works/510022), which is an MCU Steve/Tony fic in the style of The Time Traveller's Wife.
and Back to the Start (http://archiveofourown.org/works/1792207), which is set during Avengers vol 5. Steve/Tony.
no subject
Not on AO3
Given that you've read the Resurrection-verse you may have found this already, but Elspethdixon and Seanchai have a fic currently only held on LJ, which hits a lot of your buttons (Tony whump/people being BAMFs/Steve/Tony pairing):
When The Lights Go On Again (http://cap-ironman.livejournal.com/177544.html) (LONG, 616-verse splitting off from late 90s canon)
Aliens have invaded earth, and the Avengers are scattered. While Steve leads the resistance, Tony once again finds himself playing captive scientist. In the midst of a violent alien regime, separated by seemingly insurmountable boundaries, Steve and Tony have nothing to keep themselves going but each other.
Valtyr also has a non-AO3 fic:
Conjugate (http://kijikun.slashcity.com/Conjugate.htm) (Medium-length, 616-verse from around the start of New Avengers)
The New Avengers get their powers switched around. Peter sniffs people. Steve sticks to things. Logan lies around and drinks beer. In a surprising twist, Steve and Tony make out
Brain-delete
Have you read Without Irony (http://archiveofourown.org/works/148868) by tsukinofaerii? (58k words over 2 fics)
Sometimes, when a drive is completely broken, the only thing to do is wipe it clean and start over
Other things set during this period:
The beginning is always today (http://archiveofourown.org/works/817306) by marinarusalka (18k words)
After the siege of Asgard and the defeat of Norman Osborn, Steve is busy with his new duties and Tony is busy establishing Stark Resilient and working on the new Iron Man armor -- until Tony is accused of murder. Now Steve and Tony must work together to clear Tony's name. If only they can stop arguing for five minutes.
Sea Stars (http://archiveofourown.org/works/9945) by Muccamukk (42k words)
Steve comes back to life somewhere entirely unexpected; Tony doesn't remember being a hero; something is rotten in the province of British Columbia, and the 2010 Olympics are doomed.
This one is set a little later, but I'm recommending it on the basis that it's got plot, porn, whump and BAMFery:
America Isn't Chicken (http://archiveofourown.org/works/860801) by Amuly (130k words)
After a Civil War, death, rebirth, a takeover by Osborn, brain deletion, and the fall of Asgard, Steve and Tony might just be starting to get back on solid ground with one another. Things aren't perfect, not yet, but they can be in the same room as each other without resorting to violence, and they've even managed to share a smile or two.
Seems like the perfect time, then, for Tony to try and fuck it all up with a stupid game of gay chicken.
time travel/time loops
I have over a dozen fics on my list containing some form of time-related shenanigans, so I'm not going to list them all, but I assume you've read The Twice-Told Tale (http://archiveofourown.org/works/411599), which is the closest match to what you want (MCU)?
There's also:
And Has Time Enough (http://archiveofourown.org/works/510022), which is an MCU Steve/Tony fic in the style of The Time Traveller's Wife.
and Back to the Start (http://archiveofourown.org/works/1792207), which is set during Avengers vol 5. Steve/Tony.