Here's an example of upgrading:
My Lugia (Holofoil) - Neo Genesis + Something else you want for your 1st edition Luga (Holofoil) - Neo Genesis.
I understand Raikou and Dustox aren't worth very much so that's cool. Here's a list from your haves that I like:
Jungle:
Clefable (1st edition)
Flareon ( 1st edition)
Jolteon (1st edition)
Kangaskhan (1st edition)
Nidoqueen (1st edition)
Pidgeot (1st edition)
Victreebel (1st edition)
Wigglytuff (1st edition)
Neo Genesis:
Lugia (1st edition)
Only if you still have this of course.
Edit: I do have Kingdra ex and Rayquaza ex (Promo?) that I'd be willing to trade.