Hello, that's an impressive an informative first post,You are on right track as you have realised that it is best to get the correct parts to begin with, I cant answer all your questions but I'l have a stab a few.

I think you will struggle to make a single machine that can mill Ali, cut wood and do PCB work. I think you will need to consider a changeable spindle drive /motor. Ali requires low to medium speed with high rigidity. Wood needs high speed and good to high rigidity and pcbs need very high speed and super low runout. A spindle to meet all of these requirements is going to be very expensive if it existed

1) Mill plate clamp? I have never milled, manually or CNC before. Do you have to clamp down the piece, I assume you have to do something to prevent it from moving, how is this generally done, what do I need to make this happen?
Depends on your bed, T slots are best as they have a good selection of clamping jigs and tools. sacrificial mdf bed means you can just screw the material to where ever needed but not to good for Ali. Pcb work is usually held by vacuum or double sided tape. Again a range of possibilities for one machine.

2) Mill/motor? Do I use a regular router, maybe a variable speed router that I can mount on my X axis? Do I just get a regular DC motor that can be controlled via my control board? What is the best method for this?
A router cant be controlled to easily by mach and wouldn't be any good for Ali or pcb. see above for spindle problems.

3) End stops? In 3D printing, we use end stops to Home our axis' so we know exactly where our position is. Do I need something like this for a CNC mill?
cnc uses limits switches as end stops to prevent over travel and movable home switches to set the start points.

5) water/coolant system? Is this needed for aluminum? If so, how do I go about this? I have no idea on this at all.
Ali needs coolant to prevent build up on the tool and wood will need extraction or jetting to remove chips to prevent re cutting of chips and tool wear.

Good luck