I have good contacts to the "phantomstaffel" of germany. Their F-4s are about your size, so i can get you their experiences.
A german air force F-4 squadron is also based near my home, and this is where i spent my time during the military...

To your questions:

3.) The engine is mounted with 3,5 deg down attitude in relation to the fuselage reference line. This is unneccessary in the models, however a slight down-thrust comes in automatically because of the low nozzle position.

6.) the F-4s i've seen all had negative AOA and rotated smooth. Do it up according to pics and scale documentation just like the real thing and you'll be fine