Hi all I am a newb GM and I need help.
More so than most on here, I'm in the same boat. Only been GMing for 4 sessions, so hopefully my experiences will be at least a little relavent.
How do I handle Players getting contacts in game?
If they want to get an NPC during "downtime" between action, I would treat each point of Loyalty or Connection as 2 karma. And I wouldn't let them buy more than loyalty 1 in this manner.
If they're dealing with the people in-game, use your judgement, that's why you're the GM. Decide when/if the players have done "enough" for the NPC that they want to keep in touch. The relationship between the new NPC and existing contacts can also be taken into effect. That Fixer to whom your Loyalty 4 bar-tender contact introduced you to is likely like you faster than some guy you met on the street. After all, you've already got an in.
Tips for noob shadowrun runs?
You know, I can't argue with Kot on this one. Keep it simple, gritty, and make them work their way up the food chain.
How to generate npcs for combat that should rarely happen I hope?
When you're looking at mooks, either lift them from the book (and the other sources people have already mentioned). Or, if you're looking for that "something special" to make the mooks from your gang stick out, start with a similar mook, of the right professional rating, and start tweaking. One-for-one swaps work nicely (Automatics for Longarms, Unarmed for Pistols, etc). When picking gear, try to imagine what would be the realistic resources of the group for which these mooks work.
If you more mean "meeting with a contact of a contact" NPC's and you don't intend to have a fight, don't stat them. Just consider which pre-stated mook or 'runner is a "best fit" for the character in the event a fight does break out. Then, when you're RPing said NPC, make notes of the skills you're suggesting he has, how smart/dumb strong/weak, etc as they come up and he'll stat himself (if you ever need to).
As to prime-runners who are supposed to be big-baddies (or future allies), but they'll be encountered in a thoroughly non-combat environment, the same method works, but try to decide how they rate compared to the players (inferior, equal, superior, superhuman; pg. 284 - 285, SR4A) and build them accordingly before you need to use them in a fight. This is a bit more fair to the players than just assigning stats based on "feels right", since you eventually expect them to be trying to kill each other (or helping each other kill someone else).