Advice for a tight international connection

thats plenty of time for a domestic to international flight. If it was a short connection internation to domestic and you had to go through customs then it would be an issue.

The only issue will be a lack of time to stretch and relax between a 4 hour flight and a 12 hour flight.

Assuming no significant delays out of IAH, absolutely nothing to worry about once you're at SFO. Guessing you're coming in on United, so you'll arrive in E or F concourse in Terminal 3. Whether you're departing SFO out of A or G, on-time flight plan will leave you more than enough time without stress.

I'm not sure why you're connecting at all. There's a direct flight (UA7) to Narita every day from IAH. ANA has a flight direct to Haneda every day, too.

The venerable 777-200 on the IAH to NRT route has been replaced with a 787, too.

For your original question, you'll make the flight out easily. If your return trip is also through SFO, you may be at risk clearing immigration on way back. SFO had an amazing capacity to do stuff like close the Mobile Passport Control desk, which is what I count on, when there were a thousand or so people landing within 30 minutes of each other.

You're correct and thanks. Just wanted to make sure I wasn't going to have any issues as it seems it's likely they'll start boarding before I make it to the gate.

You are fine. The flight will board 45 min before departure time. You will have 45 minutes (+30) to move to the flight. Outside if a big delay, you are fine.

I had a 45 minute layover in Dallas a few weeks ago ahead of a GRU leg.

The bigger planes take a while to get everyone on board. That doesn't mean that you have to be at the gate when boarding begins. You just have to get to the gate before boarding ends.

In other words, you have lots of time, and there's zero reason to be nervous.