Can you still get on Nintendos network and E store once you do the mod?
Yes. Assuming you don't get banned via say, playing a game online before its release, you can do whatever you want (* for now -- yes in theory Ninty could do whatever they want and ban you, but for now they're not)
Hell, one of the Homebrew apps lets you just straight-up download games from Nintendo's servers free if you're a horrible horrible pirate.
And to answer the OP: It's not hard at all if you follow the guide, just involved (and I did it on an older version of the game, when it took much longer). Plan a couple hours with all the backups, and there's one point where you don't want to let it go to sleep if you have an N3DS... but it's all laid out on the guide.