My threedonedonedoone biggest complaints about the battle:
-The beginning (as has been discussed).
-How you sacraficed your metagross. It could take a hit (just like scizor), but presumably had eq, or some other attack that could OHKO.
-How you sacraficed your flygon. Especialy knowing that you have such trouble with jolteon.
What I would have done is switch in salamence. If it waterfalled, you could take it out then (or the switchin) and later have a clean up sweep with flygon (who could take down ape and jolt without a problem).
If it used ice punch, you bring in metagross and get to set up agility.