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There is no PS2 emulation for JB, you would gain nothing as of yet if you have jailbroken the backwards compatible one, so you lost nothing with JBing the other one.
This is just my experience, but Gaia is pretty much perfect, it does everything you need, and in the simplest ways. There wasn't one time where I needed another manager to run a specific game, and when I did try another one they just brought a bunch of problems.
Not much to say on your third point, getting an internal is the best option, there is absolutely no gain in using an external one. I put an 500gb one in mine, and now use the PS3 original hdd as an external to copy from my PC to the PS3 (it IS faster than non-gigabit FTP).
You have to search for emulators you want yourself, I don't know of any other tools that are really needed.