1) So... you run Hi Jump Kick / Drain Punch / Crunch / DD? That just doesn't seem very effective to me. You lose to a few key Pokemon. Salamence, Dragonite, Gliscor, Thundurus, along with the stuff like Parasect (rain stall), Venusaur, and Amoonguss. It seems like Ice Punch or Stone Edge would be better instead of Drain Punch. I've never tried Drain Punch though, so I can't attest to its effectiveness but I do know Ice Punch comes in handy quite often.
2) Yes, I agree with this point. Regardless, it's not about looking into the Pokemon, it's about comparing the effectiveness of each comparable set. Instead of trying to ask yourself which is Gyarados' best set, bulky or DD, you should be asking if DD Gyarados is better than DD Scrafty, which in some cases it is.
3) I do it all of the time and I never have trouble. Bad poison takes it down super quickly and with fighting resists on my team it rarely can prolong its demise with Drain Punch. I love Protect btw, so I often use it on two Pokemon and switch between them.
4) I said you Rest the turn Latios attacks, leaving you at 100% and Latios at -2. If you wake up due to Shed Skin, you can use Bulk Up since they will probably switch out.