overall yes it should work
the 002 only accepted up to 48k sampling rate into the adat port the 003 may be the same. This is not a problem but something you should be aware of
yes you get 12 pres. With the new version of the 003 your would get 16
use either for clocking, see if you prefer one. You probably will find neither one is significantly better than the other
The mackie controls run natively for logic, but emulate another (quite old) controller called a "hui" for pro tools. In theory it should work but some people have issues. Perhaps you should consider getting the 003 controller version instead of the rack 003 and mackie controller, it'll cost about the same but be designed with pro tools in mind and be a simpler setup. Thats what I'd do if I was using it with pro tools.
you'll get a bit of latency with a firewire device but it won't be too much, it should be bearable. There is a low latency mode I think with the 003 for tracking
btw. The mackie 800r is an excellent piece of kit for the money
hope that helps
narco