If you go with Modest on Sceptile and HPfire, there is no point maxing out speed, since you will still be slower than Modest Kazam. 330 speed should be the absolute limit, but anything above 307 will usually suffice. Timid, however, will probably prove more beneficial.
Rest is good on Milotic, since it abuses Marvel Scale and is more or less recover/refresh in one.
I like Rhydon to have around 142 speed to hax Regis and -Spd Swamperts, but that's just me. In any case, I'd say take 16 off defense and raise Rhydon's HP to the next leftovers threshold.
Metagross without earthquake gets eaten by other Metagross and Magneton. I don't understand the need for shadow ball, Meteor mash does nearly the same damage when shadow ball is SE. HProck is kind of a waste IMO. Other than for Gyarados, it has no use whatsoever. I'd much sooner have slude bomb for general attacking, haxing Ludicolos and the poison chance. HPfire is also viable if you hate Skarms.
There's nothing like a 200 speed Machamp to outspeed undanced Gyarados, Milotics, Skarms, Magnetons, Metagross, Weezing, Ludicolo, Claydol... you get the picture.
Swellow will always be a Dodrio wannabe unless it is jolly - to outspeed Mr Timid Kazam and friends. Also note that 380 odd speed > most agility Metagross and single danced Salamence/Gyarados. Jolly also means you can ditch quick attack for something else if you want, maybe facade *shrug*
Heracross laughs at this team =[