I'd agree with Ketchup on this one. Modifying the base exe's is easy, as you can quickly do that to pass them by AV's. It's a pretty common tactic, nowadays. I've done that with netcat and other tools to insert them through a box I've compromised with msf. However, if you want to pivot, you have many more files and such that are involved, and a lot of the AV's are using a more heuristic approach (finally...)
Pushing a single agent, that gets past the AV, and is capable of performing the same functions, would tend to be both cleaner and easier, and cleanup is simpler, by removing the single agent from disk / memory.
~ hayabusa ~
"All men can see these tactics whereby I conquer,
but what none can see is the strategy out of which victory is evolved."
- Sun Tzu, 'The Art of War'
OSCE, OSCP (Former - GPEN, C|EH - both expiring / expired)