My opinion on the Pre-Heresy stuff is that you should do a Legion that changed armor color scheme after the Heresy. I know that there is so much more to Pre-Heresy modeling and painting, but there isn't tons of difference between Pre-Heresy Ultramarines (for instance) and modern Ultramarines; maybe different looking power armor and definitely different looking terminator armor. I just don't think it has the same impact as seeing that Pre-Heresy color scheme on the miniatures.
That being said, I would say the first thing to do is pitch the armies that didn't change schemes. You can always go with a traitor legion that didn't change schemes, as just the completely different look with the same color scheme can still give the 'Hey, neat!' effect, but I am not one to go only part of the way on a project like this. This leaves, I believe:
Dark Angels
Emperor's Children
World Eaters
Death Guard
Thousand Sons
Luna Wolves/Sons of Horus
Word Bearers
Now, from here you would want to decide what codex you would want to use to represent the tactics and organizational structure for the Legion you want to play. My suggestions are as follows:
Codex: Dark Angels
Dark Angels
Codex: Space Marines
Emperor's Children
Death Guard
Luna Wolves/Sons of Horus
Codex: Blood Angels
World Eaters
Codex: Black Templars
Word Bearers
I specifically didn't assign the Thousand Sons as I don't feel there is a codex that would allow you to truly represent the usage of psychic talents by those throughout the legion, so you could kind of use whatever. If you want to be really clever, you could use Codex: Eldar. Even though the armor saves wouldn't be comparable to those of the standard space marine for the standard foot troop, and the weapons are different, the book really kind of covers everything. The aspect warriors could easily represent the different squad types, while Exarchs can represent the low-level psykers that would be coming up through the various temples, with the Exarch powers representing the psychic powers they would utilize in combat. Warlocks would be the mid-level psykers with Farseers being the temple masters. Wraithlords and Wraithguard could represent the war machines that were psychically guided in the Thousand Sons novel, and the legions (not just the Thousand Sons) even employed jet bikes during the Crusade. The only thing that stinks is the tanks don't match up all that well.
My personal favorite choices for Pre-Heresy projects are Thousand Sons (for creative army composition options), Word Bearers (for uniqueness; they seem to be the least done in these types of projects), or World Eaters (I happen to think the Blue and White color scheme is really sharp.)
As far as finding the color scheme is concerned, you can just go to
http://wh40k.lexicanum.com/wiki/First_founding and click on the link for each legion to see its pre-heresy scheme.
The only real conversion ideas I have involve terminators.
http://itkovian.blogspot.com/2009/08/pre-heresy-terminator-shoulder-pad.html has templates for Pre-Heresy terminator shoulder pads for use with a tutorial linked at the start of the blog post. My opinion is that Chaos Terminators make the best base for Pre-Heresy terminators as long as the chaos iconography and spiky bits are filed off of the armor and weapons.