If your legs are good, then go for the run. I suggest at least 1 day where you don't do anything at all, to give everything a break.
My first week, I didn't sub either... and that is ok, it hurt enough. :) First bit of advice on the workout page is 'start slow'. So it did not sub until week 2, so I went from 26 to 21 rounds W1 - W2... but did 3x's as many negatives.
If necessary, pause for 30 seconds before the next round of negatives, give yourself a break. Maybe pause 2 minutes then start going again. Whatever it takes to make sure that each one actually counts. I didn't learn this for a few weeks, and burned out my Central Nervous System on negatives. Now I do bodyrows with homemade rings ($15 total, see my log for how and pictures) which is waaaay better.
Anyway, enough about me. Welcome, hold off on 3:1 till week 2 and your upper body gets use to this type of workout, and enjoy!