Please allow me to suggest that the only stupid or silly question is the one your don't ask! Aviation isn't an entirely simple and straightforward activity, and there are a lot of moving parts in this activity. I used to feel like you do about asking the questions you think you should know the answer to. I took some time off of flying for a while, and when I came back I was about a decade older and more grounded in my thinking. I fly with instructors more than I need to, and ask them more questions than I probably need to. Being a better pilot involves seeking out these answers, and I don't care if a CFI thinks I'm dumb for asking
With that said, I'm sure that Class D stuff will come to you quickly. I was kind of the opposite. I did all of my initial flying out of a Class D, and I'm flying out of a Class D now. For me it seemed like learning the intricacies of non-towered airports was more challenging for me.
Here's how my usual communication goes at our local Class D (and I know we have some controllers from my tower on this site, so hopefully they'll chime in with any information concerning things they don't like about my method). NOTE: I'm just a GA pilot having fun, and I'm not an ATC operator. But, here's how it goes for me (and this will hopefully answer some of your questions about takeoff):
This is from initial call-up on the ground frequency (121.7 at my field, KBJC):
"Metro Ground, Cessna 12345 is at (place on airport) with Foxtrot (or whatever the current ATIS information is), taxiing for a VFR departure to the north"
"Cessna 12345, taxi RWY 30R via Romeo 4 and Alpha"
"30R via R4 and Alpha, Cessna 12345"
After taxiing I do my run-up and pre-takeoff checklists, I then position at the hold-short line for my runway and call the tower (118.6 at my airport)
"Metro Tower, Cessna 12345 is ready for takeoff, holding short of 30R"
The reply varies, but it is usually straightforward and consists of something like:
"Cessna 12345 hold short of 30R for traffic on final"
or
"Cessna 12345, lineup and wait"
or
"Cessna 12345, cleared for takeoff, right turn approved"
or
"Cessna 12345, cleared for takeoff, fly runway heading"