I'll break it down for you.
First, the clips are the same. Get the complete rifle. I have seen many CMP rifles and they are coming in pretty nice shape. You shouldn't have to replace anything. The wood may be a little boogered up, but you can live with that. If not get the rifle minus the wood, you will have to get a sock set and stock metal which will put you over the $500.00 price for the whole gun but the rifle will look much nicer with a new Boyd's stock. I would keep it in .30-06 until the supplies of surplus .30.06(aka M-2 ball) runs out. Who knows when that will be? Surplus .30-06 comes in sporadically. Lately there has been a lot coming in from Yugoslavia. As for the price comparison, it's hard to say since I can't remember what I paid the last time I bought .30-06, suffice to say the surplus .30-06 is a little more expensive than surplus .308. You can find clips just about any place that sells magazines. Look for them for around .50 cents a piece then buy as many as you can afford. Freds sells complete repack kits for $7.00 each (six pocket bandoleer, card boards and clips). The CMP has great customer service, if you have a problem(i.e. bad parts, broken/cracked stock) they will take care of it post haste. Example, I ordered a few M-1 parts including a clip latch, they sent me a pitted piece of crap( not supposed to) I called them and told them what I got and they sent me a like new one , no questions asked and did not want the other one returned. I ordered some M-14 parts including a nylon sling. I was billed for it but it wasn't in the box with the rest of the stuff. I sent them an e-mail and the sent me an unissued sling, no questions asked. A buddy of mine got his rifle and the hand guards were cracked, they sent him a complete stock set that was in very nice shape, again no questions asked and no request for return of the bad parts. You can't go wrong with the CMP.
One more thing, if you're new to M-1's get Scott Duffs M-1 Garand owners guide( Fulton, Orion 7, U.S. Arsenal etc.). It's everything you will need to know about the care and feeding of your rifle.