I heard from another guy that uses the gallon jars that when they are new you really have to clen them well because of some sort of residue from the glass manufacturing process. Once they are really scrubbed out well and rinsed with DW you should be OK.
You should be able to run the silverpuppy all the time, I did when I had mine. Clear jars are fine. Mine are exposed to light all the time, no problems if it's good CS. I use a big funnel for pouring out of the gallon jars, works well. If you want to spend the bucks you can get scientific grade large beakers that pour like a carafe. ebay?