Most of this stuff we don't know, as CA regards their formulae as trade secrets. They did tell us the formulae for STW and MTW (basically the difference between attack and defence determines kill chances, after many potential situational modifiers), so we might have a reasonable idea on some points - but they also told us they had changed the formulae dramatically with RTW.

I believe:

Tetsudo apparently makes you vulnerable in melee.

Wedge raises attack, lowers defence.

Phalanx probably allows more ranks to support the melee, perhaps raising attack and especially defence (pikes did that in MTW anyway). I wonder if there's also a funky "stand-off" effect at work, so that phalanxes can sometimes wipe out hastati etc without the enemy doing hardly any damage.

Height raises kill probabilities of those with the advantage and lowers them of those below.

Other terrain advantages - e.g. good or bad in a desert etc - probably modify attack.

I doubt ranks raise morale. There's a "push" effect to do with mass that gives ranks some value in stopping penetration (esp. useful in stalling cav charges).

I don't know about yelling but guess it's an attack boost. (Morale would make sense too, but I don't know).