You definitely are not eligible for the complimentary domestic upgrade benefit if your AA# is not on the reservation.
The other stuff is YMMV, it typically will not be a problem to board with group 1-2 although i would be prepared for a potential chat with the GA when you go through to explain your situation.
And similarly for seats if you call AA or speak to an agent at the airport they will most likely help you out and put you in MCE/preferred for no charge although this will depend on the agent.
AA put it in the "rules" that if you want your AA elite status benefits you need to have your AA# on the reservation .