I've got the forks opened up and draining into an oil pan, is there anything else I should do to clean them out?  Was thinking of spraying a slight amount of brake clean into the things then after a couple minutes turning them over again for a day to get any heavy gunk out of the bottom. 

No, don't do that.  The brake clean will eventually affect the fork seals, and the plastic retainer at the bottom.  The best thing to do is to pour some clean fork oil in and dump it out again.