None of those variables is a set numerical bonus. They are dynamic bonuses.
- your caster level, could be 1, 2, 10, etc;
- your wisdom bonus, could be +1, +2, +10, etc.
The keywords here are feats which allow you to apply a set numerical bonus.
if you have other feats which allow you to apply a set numerical bonus to any aspect of this spell (such as Spell Focus, Spell Penetration, Weapon Focus [ray], and so on), double the bonus granted by that feat when applied to this spell.
That excludes nearly all metamagic feats (those that increase the spell level), that is already covered by the first part of the feat:
you may apply any one metamagic feat you have to that spell without affecting its level or casting time, as long as the total modified level of the spell does not use a spell slot above 9th level.
So, that already covers nearly all metamagics and feats that are a variable bonus.
I think feats that increase the CL of magic missile (like spell specialization) should be doubled, too before using resulting CL as BAB for the trip, right?
If it's not a metamagic, yes.
For instance, these feats would get their bonuses doubled when casting the Perfected Spell: