Sapphire, My first Nuzlocke Run: Intro & Rules

So against my hesitation for so long, I decided to give the whole Nuzlock run a try.  If you've never heard of a Nuzlock run before it basically involves playing through a Pokemon game with the main rules below.  I also added a few custom rules to either make it less annoying on me or add an interesting twist.

Rules of Nuzlocke:

You are only allowed to catch the very first Pokemon you see in a route.  You make it faint, tough luck, you don't have Pokeballs tough luck.
If a Pokemon faints in battle it is considered dead. It must released or boxed and never be used again the rest of the playthrough.
If all your Pokemon faint, it's game over.

Custom Rules:

Poke Center as Business Clause:

I am allowed one free heal the first time I come to a town and 1 free heal for each new Pokemon I catch.  After that I must "pay" 300 poke'dollars/yen to use the Pokemon Center. (This means I have to toss 1 Potion from my inventory to use the Pokemon Center.) Home does not count as a Pokemon Center, and I can get as many free heals as I want there but of course that will only be applicable early on in the game. When I'm anywhere beyond Petaburg Woods, plot-wise I am not allow to go home just to heal.

Species Clause:

I think I will allow myself to catch more than one Pokemon of the same kind.  However, I am only allowed to use one Pokemon of the same species at a time on my team.  Any extras have to be boxed and can't be withdrawn until the first one dies or for the purpose of HM moves.

HM Execption Clause:

If I have a Pokemon that can learn an HM move I am not allowed to catch an HM slave, it has to be taught to one of those Poekmon.  If I don't and it is required to advance through the plot of the game, then I am allowed to catch one Pokemon to use for nothing but progressing the plot. Once that point has been reached it must be released or never used again.

Shiny Clause:

If I'm lucky enough to find a freakin' shiny in this run I'm gonna catch the freakin' shiny!  Even if it breaks the main rules.  However, I will not be using it within the actual Nuzlock run if it breaks the "catch only first Pokemon per/route" rule.  It'll act like a prize for when I finish the run.

I'm a newb Clause:

This is my first time playing this type of challenge so I reserve the right to bend the custom rules as I feel appropriate.