1) What is the difference between a CAP and a RAP?
Tons of good answers in this thread so I won't go into details on that other than.. If you need to reach the controller across internett then you need RAP (tunnel traffic using IPSec to the controller). Campus AP is on the same LAN/WAN network as the Controller and terminate using GRE.
Difference-Between-Campus-AP-and-Remote-AP-Where-we-deploy-them
You need the same licensing for both types, but a Controller can handle 4x as many RAP as CAP. So if you dedicate a 3400 controller for RAP you will be able to connect 64 x 4 = 256 RAP. If you mix CAP and RAP you will have to do your math so the total isn't above 64 CAP - like 30 CAP and 34*4 RAP.
2) Are the any Aruba documents that explain the controller licensing overall?
Overall? Well - this will give you a list.
So normally you will at least need AP and PEF-NG (firewall license) in equal amounts. Without the PEF-NG you can only have one SSID - like a plain guest network with allowall access.
2) We have 49 APs active on the WLC made up of 6 x AP105 and 5 x AP68's 38 x AP65 however the the controller is showing 46 CAPs and 3 RAPs. What defines when a CAP license entry is used compared to a RAP license?
Well - the Access Point is provisioned as a RemoteAP and is listed as such. There used to be different licensing for CAP and RAP back in pre 5.x, but not since then.