Sudonimus, can you rephrase the question?
Basically where do I put the mod in which Spelunker and Shoppy are switched?
In my own mod (Matrix Spelunky) or another mod (any other)?
The agent some morph in from one of the enemies in the level, like the matrix.

You need wall runs too
Maybe agents shouldn't be frozen at all.
And yeah, if I can, let the nearest enemy morph to an Agent
after the timer goes off.
They can move at least 2x as fast as Shoppy, have
pistol (with high-speed shooting), unkillable (until last
level, where Neo realizes he is the One), and...
probably 3x the amount of bullets as Neo.
And in Matrix Spelunky, there are limited bullets to guns
(like arrows).