Hi Clark,
There is no version in CRS as 3.1(5) and hope you mean 3.5(1).
1. When you upgrade from 3.0(3a) to 3.5(1), you cannot use the same license files. You need to order for the upgrade license. Check with product management team for more infromation(ask-icd-ivr-pm@external.cisco.com).
2. Refer the compatibility matrix to check if you have the correct version of CallManager.
http://www.cisco.com/univercd/cc/td/doc/product/voice/sw_ap_to/crsmatrx.pdf
Q#1 : Is reporting effected?
Ans : Refer the release notes of CRS 3.5 to know the newly added features...
http://www.cisco.com/univercd/cc/td/doc/product/voice/sw_ap_to/apps_3_5/english/relnote/index.htm
Q#2 : Does CAD need to be uninstalled and reinstalled on their desktops?
Ans : YES.
Q#3 : Does the IP Phone Agent service need to be reconfigured?
Ans : No
Regards
Yogi