I don't have the answer unfortunately
Alright, I guess I'll have a crack at it.
Perpendicular should immediately scream "dot product" at you. Dot product vectors CD and BE which would then equal zero.
So, CD.BE=0, (AD-AC).(AE-AB)=0 -> expand this
Make AD.AE the subject so AD.AE=AB.AD+AC.AE-AC.AB
Since AB || AD, and AC || AE dot product is product of their lengths. Dot product of AC.AB use your formula - lengths should be 2r.
cos(theta)=AD.AE/|AD||AE|=[2r*r+2r*r-cos(theta)(2r)^2]/r^2
5r^2cos(theta)=2r^2+2r^2=4r^2
cos(theta)=4/5
theta=arccos(4/5)
Apologies for the non-latex mess.