Get your umbrella out because it's Bubble bursting time.!!!!!!!!! . . . It's "Flange" not "Flanges" but must admit "Flanges" are much more fun to slap your nuts on. Don't worry Jonathan won't Flame you regards your Flanges he's no experience in this area he's never been near one . .

Welcome Andy

Your plan to build frame first before buying rails/screws etc is actually a good idea and something I tell people to do if they can wait.
Often I see people order screws & rails etc then set about building frame while they arrive only to find they either built the frame too short/narrow or vise versa much too long/wide. Often they will buy screws too long and rails too short realising if the rails where just that bit longer they could use all the screw.!!
Doing it your way then you'll know exactly whats required has you can measure direct off the frame.

Best advise is make a clear plan and stick to it. Pick a cutting area that is reasonable and don't chop and change.
Drawing in Cad is good for giving a general idea of the machine and to see if things catch etc but don't get carried away, Better to do it rather than not has it can highlight things you wouldn't other wise see but taking it to the emph degree just wastes time so just use it to rough out the design.

The single most important area of the frame are the Rail mountings. If you build in some adjustment for the rails then they can be shimmed and tweaked into alignment or parallelism without too much problem. The bed can be surfaced flat and true after it's built and so long has the rest of the frame is some where near square and true then you'll be fine.
Very important is strength and ability to resist resonance. Resonance is the enemy of finish quality so anything to reduce it helps.

Reason you see tall gantry sides on wood machines is because it leaves the bed relatively free for loading from all sides where has tall sides limit loading material from front or rear.
To be honest on Wood machines then it's not really a problem having tall-ish gantry sides has it doesn't need to hold high tolorences compared to machine for harder materials like Aluminium. Obviously there's a limit just like having too much Z axis extension will affect quality of finish but so long has they are strong and well braced tall gantry sides are ok for wood.

Slowly slowly will always workout better than rushed so take your time and keep your eye out for bargains, they do come up.
That said don't rush out and buy the first thing you see, esp on the electronics side. Check back here and ask questions before you buy if just 2% unsure.!

Good luck.