as for rune combinations, it's really something you're going to have to just experiment with as you start playing with the army. Rune combinations are something that have to suit your style of play, really. That said, taking the weapon rune of aiming, I forget its name now, is a good choice for your stone thrower, and really a no-brainer. The trick with runes is to not forget who has what - I know that goes for any and all magic items, but the runes are easy to forget.
As far as runesmiths are concerned, the reality is if you're up against a magic heavy army you're going to be out done no matter what you take. In a 2200 point game you can't afford more than a single runesmith anyway. So you've got to prepare to take a beating during the magic phase, unless you can give runes to give your troops magic resistance, but I think there are more worth while runes out there.
large blocks of warriors are a solid choice - I frankly think Dwarf Warriors are the best basic troops choice in the game, for what they cost. Hardy little blighters. Taking one as a unit of longbeads will help, esp. against a shooty/magic army (stops the spread of panic), plus great weapons are awesome. It obviously depends on the size of your game, but if you're taking all 50 warriros in a game, I'd take either two blocks of 25, or, one unit of 30 and then two units of 10 to use as bait and counter-chargers. The miners are a great help with that with their great weapons (though I wouldn't bother deploying them underground, their ability is too unpredictable for my liking. I usually just put them in my line). 25 miners in a 2000pt game will be a bit much, but *meh*.
That's a lot of thunderers. I'd say 2 units of 15, eight in the front rank (or buy/convert two more models and have 2 units of 16). You could also take 3 units of 10, but if you deploy them in a single line then they'll become less effective faster than if you have a rank to take away from (going from 10 shots/turn to 6 in one turn is painful, but with 16 and a rank, you stay at 8 shots/turn for 8 casualties). This is a no-brainer, but if you're new to the game, then it doesn't hurt saying this here: as with all shooting in this game--CONCENTRATION of firepower. Pick your targets based on where you think your best chances of causing at least 25% casualties are (for causing panic--if it's close to several other low-leadership units, all the better)--and then fire everything at it...all your thunderers, and your cannons/stonethrower, until you've caused enough casualties for a panic test. I'd give your thunderers great weapons, yes. They're great a shooting, but what happens when your opponent's forces get into combat range? Suddenly you've got fists...great weapons will at least allow you to take a few of the gits with you.
take the Gyrocopter, ignore Dogs of War. The Copter can be used to slow down the march moves of knights on the flank, and what have you, which allows you more time to shoot them

, or concentrate on other units.
Anyway, hope that helps--I *did* say a lot that is kind of basic knowledge, but I dont know what to make of your "just getting into
WHFB", so more specific stuff will have to come later