If you make your pokemon to hold
macho brace or the power EV enhancers,
or use speed stat moves like agility,
will it affect the "RUN" rate?
No the only items that effect the Run rate are the Smoke-ball, Fluffy tail, Poke-doll, and Poke-toy which guarantee running away. And No increasing/decreasing speed with status moves do not effect Run rate.
Source: Experience and http://bulbapedia.bulbagarden.net/wiki/Escape