I've just travelled South from Medellin into Quito & beyond in Jan 2008 (that's the northern most point I could get my bike to).
1) try posting a message in the Columbia communities of the HUBB for the latest information; I did & the responses were very helpful. I was informed that riding to Bogota was safe at present.
2) From the info I gleaned from other bikers, mostly Colombian, do not ride after dark & try to be off the road by mid to late afternoon. Set off early in the morning.
3) The section from Pasto to Popayan : I was advised to ride this straight through, not to stop for food or fuel (by Colombians).
4) Search the HUBB for postings about safety in Colombia.
5) Post a 'seeking traveller' message & see who turns up
The Pan Am is generally very safe.
I enjoyed the riding very much & found the people to be very friendly & helpful.
Hope this helps
when the road is straight & true, I romp ahead
when it twists & turns, I make the best I can - Lao Tsu