http://www.surdyke.com
They usually have some of the cheapest prices. However, some of the roller bearings, spacers and clips you'll have to order from your local HD dealer.
The cases use a silicon sealant. I used permatex grey. Do a google search on motorcycle engine case sealants or something and decide what you think will work best. So far I've had not issues with the permatex.
I'm sure others will chime in and give you other tips.
One lesson I learned while splitting my cases and rebuilding the transmission on my 07 xb12r is that you REALLY need a GOOD set of snap ring pliers. It made a world of a difference. I learned the hard way that having the right tool for the job REALLY makes things easier!