Heaters are nice but not necessary. Just room temperature is good if you have no heater. As for cleaning solution and rinse I usually use L&R with ammonia for production type clocks and non-ammoniated for high end movements. Usually around 5 to 7 minutes will do the job. There’s a lot of controversy about using ammonia on clocks as the ammonia does cause tiny cracks on brass surfaces. There is a product out there that I’ve heard some good things about. It’s called “Historic Timekeepers Concentrated Cleaning Solution”. To rinse after using this solution first rinse with warm water to remove the solution followed by a rinse of alcohol to remove all the water. The cost for the solution is much lower than L&R. Here’s a link if you would like to take a look at it http://www.timesavers.com/catalogmain2.asp?ProductID=17864&submit1=Search
You are probably leaving the parts in the solution too long if you’re getting discoloring. When cleaning by hand you may want to leave the parts in the solution for a few minutes longer than what’s necessary for the ultrasonic but not for too much longer. I would use a soft brush to do the cleaning rather than letting it soak too long. If it’s really grungy then multiple cleaning and rinsing and pegging the holes in between each washing might be better than letting it sit in the solution for too long.
Hope this helps Don,