Screen. How big do want the image to be? What type of screen should I get? Where is the best place to buy screens? Should the screen be a permanent mount or a motorized unit?
For a dedicated theater, I like fixed screen; since this is also going to be used as a guest room, perhaps a drop down screen would make more sense to have it out of view (and touch) when not in use?
As far as size - there are guidelines based on the ratio of seating distance to screen width or height - but a lot of it is preference - go to a theater, find your preferred seat, and then estimate your distance to the screen (step it off) and screen width, and build your screen ratio based on that.
Once you've decided on which projector and screen size, then you can determine what screen gain you'll need, and start looking for screen options that fit the bill. One key decision is also whether to use an acoustically transparent screen or not - if you do, you can put LCR speakers (and potentially subwoofer) behind it, if you have the extra space to spare.
Wiring, besides HDMI and power, what will I want to have wired to the projector? Anything besides speaker wire to pull through the walls to the speakers? already heard from many members that monoprice is the place to get cable.
Yes, monoprice is great. If you have an HDMI switching / upconverting receiver, you may only need to run an HDMI and power. If for example you have a device that outputs component video but not HDMI, and your receiver can't convert component video input to HDMI output, then you'll need to run component cables to the projector too (and so on - check your sources and receiver). Also may want to run a 12v trigger line, if you'll be using it; or a serial cable if based on the projector and your needs you think you'll need it. I'm just ran 2 HDMI and power.
For speakers, 2 runs to each speaker if you ever intend to bi-wire or bi-amp your speakers (3 runs if tri-amp). Way beyond my interest, but there you go.
You may want to run cables in-wall for subwoofer / buttkicker hook-ups as well. I put 2 behind my stage for subwoofers, 1 into the front of my stage to connect buttkicker amp to, and 2 runs of speaker wire to attic for future Infinite Baffle subwoofer use.
If you have game systems that need to be hooked up (vs racked and using wireless controllers, you'll want to consider where to connect those.
If you intend to use a GrafikEye for lighting control, you'll want to prewire for that.
If you hide your equipment away somewhere, you'll need to run wiring for an IR extender. Hey that reminds me, when I ran my wiring yesterday, I forgot to add that - I think I'm short a cable.
Sound adsorption. I see a lot of threads about this, but don't understand it at all. Do I put something inside the wall, replace the drywall with a different product, or place something on top of the drywall?
Check the official green glue thread, its pretty much all there - channel hats, rsic clips, room within a room framing, staggered stud framing, double drywall, green glue, communicating doors, etc.
Sub placement. I technically have a 7.2 receiver, any idea on where to place the sub or subs? Do i want more than one?
To do it "right", you put it somewhere, and then measure frequency response, check for "nulls" and peaks, move it, test again, etc. More info than that is beyond me, I'm in learning mode in that area (among many others).
Lighting. I have not given this much thought at all, any tips on what type of lighting would work best and where to place them?
Mostly preference, many/most use recessed lighting; have to pay attention to hurting your room's isolation if there are unattended gaps around fixtures - for this reason, some install their lighting within soffits (inside the drywall shell, rather than making holes in it). Others add wall sconces as uplighting. Many add rope lighting hiding up in soffits, under stage/riser lips. Adventuous also add star ceilings.