I thought level of your pokemon didn't matter at Mt Battle and they rounded them to 50 or to the highest level of pokemon in your party?
Can you trade with Emerald directly with Colloseum or do you have to go through Ruby/Sapphire? Gonna form a team on the GBA games first, since it's easier to train EV's and you can breed.
Last, is there really no way to control your ho-oh's nature? You can't take a look at what it is and if you don't like it reset and do over?
Last, for purification please see this Deathborn 668's walkthrough on gamefaqs.com under colloseum. I'd post a link, but apparently I'm not allowed since this is my 1st post. Do a find on nature and he gives you the breakdown for which nature responds to which action. This makes a lot of difference. Of course now the only problem is you can't see a Shadow Pokemon's nature immediately. If you use an IV calculator like Serebii's you can come up with a good guess by plugging in a neutral nature (serious) and looking for the highest IV (hopefully >=32) and the lowest (hopefully <= 0) and then guess at the nature. I also used this to get the best natures for the magical beasts; though, really they're outgunned in current battling, so unless you're obsessive about it like me you should probably pass.