Thanks, any little bit helps.
Anyways, over the past couple of days I've looked back over the published run to get a better idea of how much time some of these new discoveries will be.
I'm not worried at all about running out of Mega Punches while going through the Nugget Bridge gauntlet - I would be replacing Tail Whip (a move I don't use at all in the run) to make room for Mega Punch, and I actually don't fight very many enemies I don't one hit with other moves. I didn't do any exact calculations, but should I not have enough Mega Punches to cover all the enemies I two hit in the actual run (or if I run into an enemy I *still* can't one hit even with Mega Punch), Water Gun (or even Bubblebeam, see below) would handle things.
Of course, with Mega Punch at my disposal, I would also have good reason to go with the strategy of beating Gym 2 the moment I first step foot in Cerulean City, especially with having plenty of spare Mega Punches at my disposal after coming down Mt. Moon, and delaying my first Pokecenter visit until after I finish this Gym. This also gives me Bubblebeam to help save turns against the second Rival fight and the Nugget Bridge gauntlet, and also removes the entire second trip back and forth between Cerulean and Vermilion (as I would be able to enter Gym 3 immediately after getting off the SS Anne), finally making my route through that section of the game clean and elegant.
Mega Punch does seem to have one single drawback - I would be able to survive on keeping Mega Punch around, having it eat up the unneeded move slot in Squirtle's movelist (I would thus have Dig replace Tackle, and Bite replace Bubble), through pretty much the entire duration of Mega Punch's usefulness, and up until I obtain Ice Beam. At this point, I would need to drop one of either Mega Punch or Bite for Ice Beam. While Mega Punch is 20 points more powerful, Bite allows me to save time by causing the enemy to flinch and not attack at all. I don't believe there's any time where that 20 points of damage is going to allow me to defeat an enemy quicker, especially before I pick up Strength (which will replace whatever I didn't pick anyways), so chances are I'll lose Mega Punch and continue on from that point as I had in the previous run.
Now, as for the other potential route change options.. those being Blizzard and Fissure..
I'm going to definitely say no to Blizzard; I can count on one hand the potential number of turns Blizzard can save over Ice Beam (most are against Gyaradoses), and the amount of time it takes to just learn[/i] Blizzard offsets much of it - going out of my way to obtain the necessary TM will likely erase the remainder of the gain.
I'm still heavily debating over Fissure.. sure Blastoise in general is slower compared to Onix, but the Blastoise in the run is both higher in level and has been boosted due to the large amounts of effort EXP it's obtained, so not only is it faster at the start of the Elite 4 than Onix, but it's also likely I will need only one or maybe even no speed up items at all to get Blastoise faster than Lorelei's Pokemon (so that Fissure can work). Removing the need to capture an Onix also saves time, and since I'll need to bring an Ether to restore it afterwards to hit other Pokemon, I can use it later on against other Pokemon used by the Elite Four to save more turns. However, I'm going to need to find the closest Ether of any sort to the main path (and depending on how far away it is, it might take some time to get it). This likely means I'll be putting Fissure onto Blastoise, but I'll still need to do some investigation before I confirm for sure.
Now, as for restarting the run itself.. if at all possible, I'd like to be able to find out how easily I can manipulate the starting stats for a Squirtle. Since there's no obvious variation at level 5, I'd need to level it up a bit to be able to determine what it's DVs are, and to do that I'd either need to use the Rare Candies gameshark code (which is slooooooooooooooooow) or have the code to be able to pick up my starter at any level I want, preferrably level 50. I could then experiment using it, then confirm my results by obtaining the Squirtle then using the Rare Candies code to manually level it up to 50 to double check. Unfortunately I can't seem to find this code anymore (if it even existed; it might've been for another Pokemon game for all I know), so if anyone happens to have it lying around, please let me know.