I'd like to expand a bit on Stage Selection.
The method I told you about IRL - with both Teams choosing 2 stages +Smashville to make a 5-Stage Strike - I will refer to this as the 'Grab Bag Method' (because I don't have a name for it and it sounds sort of fun).
First of all, I think it works out great for 1st Round Stage Selection - plus it expands the Starter Stage List to practically any stage. You should make sure to include rules for a 3-Stage Starter (with each Team choosing 1 Stage, +Smashville).
What I see missing in the Stage Selection Details section is the option of a Stage Ban for each Team. I think this is even more appropriate (and important) to include as a solid rule, not just as a footnote or optional rule, since literally
any stage might be available as a Counterpick.
Speaking of Counterpick Stages...
I think this needs to be tweaked a bit more. Maybe each Team should be able to add in one or two Counterpick Stages to the Grab Bag. This would give 7 to 9 Stages in the 'bag' for each player to counterpick from, which is about how many you see in the average tournament.
The only problem I see with the additional one or two counterpicks is the increased likelihood of players going to exceptionally dumb stages (which might make tournaments run longer). It's sort of like MLG where having just 1 Stage Ban just didn't feel like enough due to the overwhelming number of stages (I had to play on Pokemon Stadium 2 and Green Greens multiple times at MLG just because my opponent wanted the lols). It also reminds me of the Ashland Tournaments where there were noobs playing against other noobs and they would go to Hyrule Temple (both in Melee and in Brawl) because they didn't know any better (there's nothing more painful than waiting for a TV while two noobs play a tournament match for 8 minutes on Hyrule).
I noticed that in the rules you mention that TOs are responsible for creating their own banned stage list (such as telling everyone to stop playing on ******* Hyrule). But, in my experience, TOs are generally not inclined to do much more than adopt a set of rules and then tell the players what they are (some TOs don't even do that much). This means that while theoretically any stage that could cause grief for players can simple be written out of the options, it's more realistic that they will sit around getting counterpicked by noobs and people looking for lolz.
On Port Selection:
I've discussed this with other TOs over the years. Originally it was Rock-Paper-Scissors, but it has gradually changed to a coin flip. The reason is because some people are opposed to playing RPS, while no one can argue against a coin flip. Thus the Coin Flip must be the default option.
IMO, there are still some things this rule set does not cover, but they are things that you generally don't see nor take into consideration for tournaments. What I would suggest is using these rules for general play, but having a second set of rules that cover further questions that
might crop up for a tournament. In the words of the Boy Scouts, 'always be prepared'. I've pretty much ironed out all such rules, and you can find them in the
Standardized Rule Set.
-Edit-
What are your thoughts about a Team not being able to Counterpick a Stage on which they have previously won a Game in that Set? It's always important to consider when using 'liberal' stage lists.