Re: MIM Standard Telecaster Pup changes
Ral, WELCOME TO THE FORUM!!!! There's no such thing as a dumb question, sometimes we refer folks to the search function but only because we're lazy, and unlike other forums there isn't a "noob" stigma, unless you make broad sweeping generalizations about particular pups.
Anyway, I think you'll be very happy with the lil 59 you can get some cruchy LP-esque tone in full bucking mode, and some tele twang in the split mode. I'd recommend getting a push pull pot for splitting, then you won't have to drill a hole anywhere. You will not need to route you guitar b/c the lil 59 is made to fit in the factory sized hole.
As far as the neck pup goes, that's up to you. If you like it keep it, if you don't kick it to the curb. You might want to look into the vintage neck, or maybe the Alnico 2 pro for a smoother sound.
MIM Fenders play well and sound good with upgrades, I'd really recommend getting two new pots, maybe a new switch as well, I also prefer orange drop caps but that is a personal preference. Another huge upgrade a MIM Fender is hardware. The stock bridge and tuners are fairly cheap, and with components you have an all around better guitar.
Again Welcome!
Luke