I am relatively new to posting to the zone but I have been reading it and working quietly in the backround for years. Let me take a stab at your questions.Somebody will correct me if I am way off base on any of these.
1. An industrail hobbies mill is a big leap over an x1. A good motor for the IH would probablly dwarf the x1 so that will probablly rule out the use of the same motors for each machine. I don't see this as a show stopper because when it comes time to sell the x1, even it has nothing but the motors attached, you can sell it as cnc ready or at least cnc capable.
2.Running both machines, one at a time, is really no big deal with Mach3. All you do is set up different profiles, one for each machine. You could in theory run dozens of machines up to whatever limit that Mach3 might have for storing profiles. I have a least 6 on my laptop as we speak because I use it to test stuff and then I put the machine on a dedicated computer because I like to run more than 1 at a time.
All you would need to do is make sure during the setup that the motor wires have quick disconnect capability.The only other considerations would be the motor current setting would have to be changed to match each machines motors. Shouldn't be too hard to set up different resistors and with switches make it a 2 second job. Just be ultra sure it is fool proof. it won't hurt the big motors on the little motor setting but you will and I repeat will fry the little motors on the big motor setting. With a little inginuity, it might even be possible to rig up a switch that also lights up an indicator on either machine to indicate which one is selected or even disable the motor from running unless that machine is selected.
3. If your budget from right now is $2k you should be able to get a bunch of stuff and buy it right the first time. Since you have taken the machine apart and all the other stuff, it looks like you pretty capable.
I would suggest the Gecko 203v for there protection against misswiring of all sorts and the new feature of morphing from micro to full step on the fly based on motor speed. This means you will get the most from whatever stepper that you choose.
4 Take your pick of breakout boards. I personally have only used the Candcnc mini I/O version 3 which seems to have been dropped, but their new ubob looks like a real winner with its port stretching capabilites it should prevent you from having to go with 2 pp ports for the big machine.
5.I think that everything other than the motors and limit switches can be used on both machines. Somebody can chime in here but I think the x1 setup as cnc ready with the motors attached and limit switches and zero backlash of some sort would sell for more than enough to make up for what you leave attached to it.
6. power supply. buy one that is the right size, volts and amps, for the big mill and just buy motors for the x1 that can run on that voltage. Many people wind up getting motors that we run on too low of a voltage and regret it later. Having more amps for the little motors isn't a problem because that is what the current linit resistors do, they keep the motor from drawing too much current.
7.If you go steppers (easier to setup and less expensive) then you won't need encoders.
8. In my opinion the limit switches would be so lo cost as to not be worth moving to the other machine.
9. I would talk to industrial hobbies and see what there recomendations for motors would be. They can tell you what kind of power you should be using to get 1. top performance and 2. acceptable performance if the first one is too costly.
10. It might be possible to use a triple stack nema 23 at max voltage for the IH mill and then use it with the right current settings and limit your rapids in the software for the x1. Just by looking at the IH mill and knowing what you will want to cut on it I would personally use double stack Nema 34's but that is just an of the cuff opinion on that. IH will probably chime in and correct me.
I have been suprised by the kind of power that my triple stack 23 puts out on 40v on my rounter on the z axis, lifting 2 roto zips and a large aluminum plate. I am upgrading to a 50v ps that I just purchased off of ebay to make it go faster. Based on its inductance it is maxed at 82v.
Thats all I can think of now. I woke up to the sound of a light rain am I am listing to it as I type. Time to go back to bed.