Right i'l try and help, hopefully wont have missed anything off:
First of all, your aerial is fine. It will pick up FM, AM, etc etc
Nothing wrong with taking the door cards off. With some models, a door speaker was fitted into the doors as standard.
I hate bullet connectors, instead i use a chocolate box to join cables together
Also you can run cables under the carpet easily. Remove the plastic seal around the lower half of the door, and pull the carpet away.. the cables will fit snug under neath.
Finally, if you put the seats down alot, then put an amp under the passenger or drivers seat (if u wish to use an amp), then wire that to the shelf.. you can always remove the shelf and lower the seats, and nothing will get damaged or in the way