Drove my car to work today, handled just perfectly fine. When it started getting warmed up, drops at idles, sometimes even stalls. about 8:30?

*backround information: a hose was cracked which caused the stalling and idles.
the hose is a dealer item. some type of vaccum hose.
the car has 1/2 tank of mid grade. my father did it, kinda upset about that but whatever.
But before it idled, did not stutter at any way, was cruising great! (:
Got to work, car was at about a little bit below 210 degrees. Then i had to do some work deliveries picking up transmission parts and what not. Car cooled off a bit because of the weather and the stuttering went away. about 10:40?
Took lunch, started to really warm up in weather. Turned on my car, stuttering below 1k rpm, and then i hear it turn off, make this click noise and its on again, like all in under 1/2 a sec. its like vrrrrr *click vrrrrrr. like wth?
During my lunch, went to chevron, put 10 bucks of premium and it worked alot better now!

My co workers looked at it, connected a computer to it. I had Cylinder 1 Misfire, MAF senser and some other vaccum sensor. They put a temporary fix on my hose, Got a rubber spark plug boot, and put electrical tape, and i turned it on, omg, no stuttering. it didnt go low in rpms but still was under 1k, usually when i start her up to begin my day, it does 1.5k? a little over 1k rpm. they cleared the codes and tell me to go for a drive. 5pm
Driving home, when i get to almost full stop, it starts shaking, but when it moves it doesnt. Almost to the end of my trip, it did that click thing about 3-4 times. Got home, told my dad whats going on, and he said, if i change my cold air intake mod off and replace it with the old one, all of it will go away, i disagreed and wanted to replace all the spark plugs.
My concerns are:
is the cylinder misfire causing all this?
That computer that was inside the original intake box, does that need to stay cold? because my box is half open, and im not getting cold air, ill finish when i replace the plugs.
Whats that click noise?
What sparks plugs are recommended?
I wanna replace the T-stat for my car to operate at colder temps, will that make my car more efficent? my dad says if the car was built to work at that temp, then i should keep it that way?
Thanks thanks, and more thank yous!