Let me try to organize your questions:
1) Should you match the upper brand to the lower?
Not necessarily. If the upper and lower are both in spec, you'll have no problems (my go-to AR is a frankenrifle). If they aren't in spec, you're better off getting ones that are and ditching the crap.
2) Will you have barrel or BCG compatibility issues if you mix brands?
Nope. Again, in spec is in spec. Just buy a good BCG (like Bravo Company). Whatever you get, make sure the gas keys are staked properly.
3) How hard to assemble your own upper?
It isn't hard, but it takes special tools- an upper vise block (I like the DPMS Panther Claw), a barrel wrench, and a torque wrench. Honestly, for a first timer I'd just get a complete upper (like a Bravo Company- they may be a bit more, but may as well buy awesome the first time).
That is done when the barrel maker installs the barrel extension onto the barrel. While you could have tolerance stacking issues between the bolt and barrel, in practice I've not heard of it happening and the only remedy is to replace the bolt or barrel- you can't adjust the headspace because it would mean dinking with the orientation of the barrel extension relative to the gas port. Again, buy quality and it won't be a worry at all. Unless you think you're going to get into building ARs for kicks, you'll spend more on the tools to assemble the upper than you'll save by buying separate pieces. Better to just get a complete upper (with or without BCG).
So far it sounds like you're doing OK. Keep an eye on that parts kit the first time you use it- while I have built two with DPMS parts kits, the trigger and hammer pins both were walking on me no matter what I did, and I installed KNS pins to avoid that in the future- it would have been cheaper for me to buy a better parts kit to begin with.