The tank set to LP will work fine, SLP/LP both work very well.
The stock board is fine, really no need to upgrade. You can flash to the latest software version (2.0) here if it's currently at 1.0. http://store.macdev.net/Articles.asp?ID=246
The factory settings are fine and don't typically need to be changed.
The factory Shift barrel works great. There are plenty of barrels that work really well and you'll get plenty of different opinions on something like that. You can get the insert kit here that works in conjunction with the Shift barrel. http://www.aggressivesports.net/inde...&product_id=80
I'd say the most popular aftermarket trigger for the Clone would be the VP trigger. I have never heard anybody say they don't like it.
Other than that I would just recommend picking up some of the newest Militia Lube http://www.aggressivesports.net/inde...tegory&path=73
and you should get an o-ring kit as well.