With apologies I'll begin with a brief rationale before tackling your specific questions
When using the Moltke plan I've found that the two most important things I can do at jump off are to get my forces mix right and to set myself very clear objectives as to where I want to go and why - and it's the "why" question that dominates my planning.
By using the Moltke plan I'm attempting to get a rapid resolution in the East so that I can transfer forces westward before the WE can build up an overwhelming superiority there. That resolution isn't going to be achieved by territorial gain or the progressive wearing down of Russian morale. It can only be accomplished by the complete destruction of the Russian armies deployed within my reach - and that, in turn, will never be accomplished as long as those forces have avenues of retreat into the Russian interior. My initial objective, therefore, must be to block those avenues and I can pretty much do this if I can secure the rail line running through Wladislavov via Kowno, Grodno, and Bielostok to Brest-Litovsk.
To guard against the opening up of a secondary supply line through Lublin I need my Austrians to at least hold Rawa Ruska - but I can create a much wider safety margin, and give myself some powerful jumping off points for later exploitation, if they also secure Kowel and Rowno. This can be managed without first removing the thorns of Lutzk and Dubno but if at all possible I'll take these on the march to avoid having to come back and clean up later.
With this perimeter established the great bulk of the Russian starting forces will in the bag with only time and perseverance required to eliminate them entirely. They might thresh around a bit while awaiting destruction but that can be tolerated - indeed encouraged should they show any inclination to throw themselves against the ring of fortresses surrounding them to the West and South.
Once I've painted myself this big picture the answers to the particular questions you've raised become much more obvious. So:
1) Is it advisable to bring the 2 German armies south to smash the Russians in Poland? Should I send them north towards Riga or east towards Minsk, etc., to spread out the Russians?
No and no. The function of your 1st and 2nd armies is to isolate as large a slice of the Russian forces as possible by securing the rail connection to Brest-Litovsk. Smashing comes later.
The fact that when doing this you'll be following the rail does, however, throw up an opportunity for a sideshow exploitation and the trashing of some retreating Russian units in the process. If you concentrate your super-heavy artillery (together with Gallwitz) in 2nd Army and support this with the bulk of your remaining corps you can power down the rails to your primary objective while detaching 1st Army with the heavies and an additional corps or so to grab Koschedair and play merry hell along the eastern track as far as Minsk.
While all that's going on you can similarly use your starting forces in Koenigsberg to push North. With most of the Russian eggs in the Polish basket this area begins almost undefended and if you can afford to add your cavalry corps to the enterprise, over-running Riga is not out of the question.
2) When advancing in Russia, how important is it guard rail lines? I've been using militia as they become activated, but they can be brushed aside easily. Would Cav be better for this? Corps garrisoned in bigger cities?
It's critical, but if you focus your advance along a specific axis of attack instead of an expanding front it's not impossible. If you can park two or three militia units, with a commander, inside your most exposed cities they'll normally hold out long enough for you to rail a corps or two back to their rescue.
3) Should I constantly build Inf and med art to beef up the West like I've been doing? The units that unlock after a few turns: send them East or West? What about replacement chits?
Yes indeed. The French will come at you hard and even with Plan XVII in play you'll be lucky to get past February '15 without having them hammer on you. Since you'll only be committing to a few very focused battles in the East you should be able to direct most of the unlocked forces to your western defences. I like to send a few of the more easterly located units to screen the southern limits of the Russian advance but I'm not entirely convinced that this is necessary.
When defending, tactical savvy (as in your choice of combat posture) is very important. Because it's such an attractive target to the French I tend to load Metz with as much arty (including heavies) and as many divisions as will fit, with at least one full corps inside the fortress. I'll then typically fight the first round of combat with the Balanced Deployment option to suss out how the attackers are coming at me and respond accordingly. Having high defensively skilled leaders in play doesn't hurt either.
As far as replacements go - spend them where they'll be most effective. Replacements scarcely "take" in units outside structures so you can bank a few in the early turns when every unit is either at full strength or on the move. That way when you need to rest your spearheads or restore a defensive position you'll have the necessary numbers on hand.
4) Is it smart to place whole corps inside armies for extra power, or is it better to spread out corps and rely on MTSG? In the West, I've been placing corps inside armies, but I'm wondering if loose inf would be better, with corps in a separate stack (but same region)? Not sure on the ins-and-outs of this.
I'm not sure anybody is sure on the ins-and-outs of this, but I tend to follow your line. As I see it, the trouble with loose arrangements is that corps can be individually "picked off" during the battle and thrown into retreat so that your combat power can be dropped in lumps rather than gradually eroded.
Sorry about the volume of the response - just hoping that somewhere in all of that you find something helpful.