Personally, I price out the runs using the following formula
Get a base price for the general kind of run, from 1,000 Y (Courier) to 20,000 Y (Extraction / Kidnapping). If a run involves multiple points, add the base prices together.
Add +(Total Street Rep x 5)%.
Subtract -(Total Notoriety x 15)%
Add or subtract other modifiers based on location, difficulty and prep work (between -50% to +100%)
This is the total maximum price the Mr. Johnson is willing to pay.
Start Negotiations at 50% of that with each net hit on a Negotiation test changing +/- 5%.
This method enforces the idea of a runner's reputation getting the higher paying jobs as well as screwing up costing in the long run (Street Rep vs. Notoriety).