sorry ive been stupid amounts of busy recently...

i have no trouble with my CDs in the lower slot.. however i dont have stock shift knobs, my new auto shifter sits about 6" lower than the stock one.. and my 4wd one sits about 2" lower than stock... ive never had a heat related issue with having my head unit mounted down there.. the engines computer is right there.. if there wasnt adequate ventilation it wouldnt be there.. plus the stock cd changer probably puts out a good amount of heat anyway... never been an issue for me but the wiring is more cramped, i had a hard time getting my wires all tucked in behind the head unit down there.. but i also have 9 RCA connections back there (1 for each speaker.. 1 for the subs.. 1 for the tweeters.. and 3 for AV input

the cubby hole could definitely go in the upper slot, there is one made for a rodeo that already has the brackets molded into the plastic so it would be easy.. only thing to worry about is anything that comes flying out of there will be more of a projectile because its higher in the air to start with

its more important to have high end stuff in the front and then work your subs to fit your budget (assuming you are looking for sound quality) a good set of component speakers in the front will provide you with a good amount of bass to begin with.. when i pull my subs for camping trips, my components in the front and 2 ways in the rear sound acceptable

the stock speakers will be fine with an upgraded head unit.. they will actually last longer at loud volumes with an upgraded head unit as opposed to the stock one (less distortion)