ebay and scrounging/borrowing are your friends!
The LBS is great for some stuff, not so much for other things.
Here is what I'd recommend:
Pedals: $125 - Ebay, craigslist, or wherever. Find a sale or something.
Shoes: $150 Your LBS - you want to make sure you get a good fit by trying them on.
Mudguards: $70 (not certain I'll get them) They are helpful, but don't spend $70. SKS chromoplastics should cost about $50.
Rear pannier rack: $30-80 Topeak and Blackburn both make nice rear racks for fairly cheap. Some people like to pimp out on Tubus or other racks, but they are very expensive, and not always worth it for everyone. Try to find a good one in the $30-$50 range. LBS or Craigslist.
Front pannier rack (maybe) See how you do loading up the rears first. If you are a light packer, you may not need fronts.
Rear panniers: $100-250 This is an area where nice ones make sense, and being able to try them out and play with them makes sense. Some people like a million pockets, others like one big pocket. LBS would be good.
Toolbag: $10-25 Borrow one from someone else, or buy one from Performancebike.com. They often have sales and sell bags for just a few bucks. Work the same as a fancy one.
Handlebarbag: $50-100 A good one you can try out makes sense. If your LBS has a big selection, go with that.
Bottle cage: $10 Don't pay 10 bucks for a bottle cage. Borrow one from a friend's bike, or buy one when you buy the toolbag from performance for $3.
Don't be afraid to scrounge, or buy used stuff. Some things, like shoes and panniers, you really want to work "for you". Other things, like bottle cages, tool bags, and to a certain degree, racks, you have a lot of flexibility on.
-Sam