Let me see if I can touch on a few points:
1. Regarding Corneria at the start...I advanced as much as I could to try and get him to move out of the way. It just came across as being quicker to force him out of the way than the latter. Perhaps I did something wrong, but I doubt it...???
2. Swamp cave...the Iron Armor for the wizards is almost a necessity. Without it...well, they tend to do 2 hits for enough damage to kill any character outright. And even with luck manipulation, I found it nigh impossible to get them both to miss, or even to 1-hit.
3. The sea shrine...I had to modify that run to hell and beyond, because of the required fights I was coming up against. I wasn't kidding when I said Squaresoft designed the random encounter list perfectly...albeit probably on accident. Running through the shrine normally (going to get the slab, then running to kill kraken), I ended up with 5 required fights (3 sets of ghosts, 2 sets of waters). This method, I ended up with ONE required fight (stupid wizard sahag), and actually gained 150 frames over my prior run. I roamed around the exit/exited+went inside the town to avoid another required fight one step shy of getting back to the airship. Could I have done it differently? Probably...and I may in the future.
4. Little plans like that (a house instead of the inn, etc.), I'd have to check and see just how many frames I lose in the process. Somehow, I have a feeling they'll be pretty close, but all these tiny "quirks" might be what is necessary to push the run under the 1:30 mark.
5. The Earth Floor...I wasn't happy about that, but here was the problem. Based on the encounter list, if I hadn't done those two fights there, I would have had to deal with a group of 3-4 fires later on, as well as a required water fight on ToFR Water. Killing two earths with a weakness to fire was a lot easier than the pair of alternatives...trust me, I tried both ways. And to touch on Axeman's comments on why I didn't do the fights earlier...well, let me quote a little blip from my notes:
ToFR 1F (Avoid 1, 2)
ToFR 2F (Avoid 1, 2, 3, 4, 8)
ToFR 3F (Avoid 3, 4, 5, 8)
ToFR Earth (Avoid 7)
ToFR Fire (Avoid 7)
ToFR Water (Avoid 1, 3)
Basically, the way the encounter list is setup, there's no possible way to avoid those required fights, short of advancing the list probably an extra 10-15 fights. Either I'm stuck fighting that streak of 5-7 required fights in a row (see my 2nd run post), or spacing them out and avoiding some of the uglier ones (Gas Dragons, Fires, Waters).
I admit, ToFR and the Sea Shrine are probably some of the most unorthodox solutions I could have done, but this run was a combination of time and lowest level. Fighting groups of 3 ghosts, 3 fires, 3 waters, or a pair of Gas Dragons....well...I guess you can call it the lesser of two evils?
I'd be happy to post my encounter list I made while I was making my 3rd run, if that would allay some of the questions you have. Other than that...I won't admit that the run is flawless, and probably never will be, but it is one hell of a start.
To be considered a country, you need to have a beer. Sure, it helps to have an airport or nuclear weapons, but at the very least....you need a beer.