*yawns*
Man, I haven't posted in these forums in yonks.
First up, Goldflash, before posting ideas for UU's, philosophies and general ideas for differentiating the very particular races and sub-cultures defined in the 40k universe, I suggest you talk at length with someone who knows Civ and 40k very well, like Zulu, Kal-el, Embryo, Omni, or even me if you're scraping the barrel
Seriously though, Check through the older threads through the links already posted. They have most of the right ideas, and combined with the obvious drive you seem to have, You may be able to get something done.
As for Races, I suggest you go with our culture/isolated tech tree concept, The 40k races just don't mix.
If you have trouble with the idea of Imperial guard mixing with Space Marines, consider it an Imperial force, which can be lead by any number of different generals. Armageddon is a good example. The imperial forces gathered on the planet were a mix of all the military branches of the imperium, marines, guard, sisters, the works. These forces would come under the command of whatever servant of the Emperor had the will to assume control, or would be requistioned to the forces that need them. This is just the same for the orkish hordes, They were all under the control of one Mr G. Thraka, but individual warlords had plenty of control.
For now, I suggest you make the standard collection of units for each subculture, and add one UU for each race, with the standard civ style of upgraded stats and maybe the odd special ability. It's going to be much easier.
When talking about Barbarians, I was always a fan of Dark Eldar, but they became subsumed into the eldar culture with the growth of that idea.
Necrons seem to be your best bit, use a necron pyramid/tomb type structure as the barbarian village, with the warriors as basic barbs, and destroyers or wraiths as the advanced version.
If you want to go with dark eldar, use a warrior as the basic, raider or a jetbike as the advanced unit, and a warp gate as the village.
As far as naval combat goes, I suggest you use BFG ships as your naval units, in conjuction with one of the Space + Earth terrain sets I saw a while back. These would fit far more in the character of the game, and would facilitate many important strategic elements in civ.
For instance, a Space marine battlebarge can sit up in orbit, and then transfer marines with the amphibious ability to represent drop pods. While it's doing this , an Eldar raiding fleet might make a hit and run attack from behind an "asteroid" (small island)
What we had to do at CNC:Generals 40k : Only war, the generals mod that I'm part of, is trim down the extensive lists in order to make a playable version that could be done in a shorter timespan. Bear this in mind.
(by the way, why didn't our site get included in the list of links? I'm most offended
http://www.planetcnc.com/onlywar )
For the goody huts, I suggest you use ruins, but disable the function of the free unit, as this will only lead to bad things.
I'll check back sometime soon, but I'm away soon, so good luck and have fun!
We might be able to use them in the mod 
