Learning how to buy Runes

I highly suggest you use this link: http://www.mobafire.com/league-of-legends/build/rune-tips-what-secondary-and-primary-means-and-more-24255

It helped me immensely on my runes choices. It also ranks runes within what is good or bad (Based on the stat you get vs gold cost). As long you get S to A range runes you're good, mix and match based on your tastes. Each champ can honestly have a rune page devoted to them alone. If you notice the S to A range is A LOT of choices still and he suggests basic runes for anyone.

Mine are:
AD Carry
AD Red
HP Per Level Yellows
MR Blues
AD Quints

AP Carry
MrP Reds
HP per Level Yellows
AP Blues
AP Quints

Tank
AS Reds (For jungling)
Armor Yellows
MR or AP Blues
Movement Speed Quints

UPDATE: Also the CDR runes are INSANELY EXPENSIVE. So if you want them, save for them but getting a full blue set is like 6300 IP. I still don't have CDR blues and I've been playing for years and have 50% of all champions in the game.

1) yes.

2) check on the list you posted.

3) magicpen red, manareg / level yellow (since they get better than the flats at lvl 7) and CDR blue. Quints depend on your role and character aswell as your laning opponent. For you playing an AP Carry, you could take AP. If you are support you could take gold/10. And yes, you could fill an entire rune page with cdr.

4) The list you presented already gives you the sorted informations you are asking for. Sorted by primary and greater runes, so exactly what you are asking for. Yes, you have to put in an effort of <5 minutes for planing a runepage.