Firstly, ordering the the grip and base separately is normal with virpil. Rather have to create bundles for every possible combination, you just order the base and stick you want and they apply a 10% discount at checkout.
As for your question, it really comes down to how you want to fly (if you were think about buying a warthog and THEN upgrading, I can only assume money isn't an issue here).
The CM2 base is not suitable for on top of the desk use, but their warBRD base is. The flip side is that the warBRD base is not suitable for long stick extensions.
You could get a warBRD base and a CM2 grip, but be warned it will still stand very tall on the desk (but to be fair the warthog is kinda tall as well). The alternative is to use their desk edge mounts (which are excellent by the way; I have 6), but you will need a second one (and mounting arm) for the throttle.
Regarding the bases, the warthog was good for it's time but the design decisions that went into it really don't hold up nowadays (the certainly don't justify the price IMO). The main problems are the plastic cup and ball articulation which is prone to sticktion and has been known to break with extensive use), and also the single spring design which doesn't delineate the axis and requires more force to maintain one axis when the other is also used. It also have a VERY clunky centre.
The virpil bases are (now) generally very good and are adjustable with replaceable cam profiles and springs. They're made of machined aluminium and have proper bearings. The other advantage of the virpil bases are that they are capable of a lot more inputs and axis. A warthog stick on a CM2 base is fully functional, but a CM2 stick on a warthog base is limited.
This brings me onto the next topic, the sticks.
The warthog sticks are good but not without their flaws. Being made of metal they're quite heavy, which means they don't balance very well on stick extensions. It also means that if you drop it you are likely to break the pot metal stem (I've had to replace mine with a 3d printed one from shapeways since the spare part is not available). As mentioned they're also limited to the number of buttons they have and have no extra axis. The F18 grips is not worth the price they're asking for it. Avoid.
The CM2 stick is good. It's light, comfortable and has many many buttons. It has a dual stage trigger, a flip down trigger (where the flipped up position is actually bindable), 4 4-way and push hats, a 2-way and push hat, 4 buttons and a lever axis that also has a simulated button at the end of its travel. The best part about it however is that is has enough buttons and hats in just the right places that you can map every button on the warthog stick in their actual locations, meaning you'd never actually need to mount the warthog since every button is covered. If it weren't for the throttle, I'd have sold my warthog by now. The only downside to the CM2 stick is probably the height if you are a desktop user.
Personally I think you;d be throwing your money away if you bought the warthog. It's only real value as I see it now is as a complete set for someone starting out and most of that value is in the throttle you don't need.
The final option is you fix your CH stick. If it's just the button gone, you might just have a loose connection. If it is the button, they can be easily replaced.
