Carl, that six gallon tank should be sufficient unless you have exceptional hot water usage. It sounds like your heater is short cycling. Yes you can flush that tank out if you want. One way is to open the tank drain plug and then connect the trailer to your city water supply and turn on the water.
Based on my Safari these should be the positions for the three valves on your water heater bypass. Note the valves are stacked vertically on my trailer.
The top valve is turned counter clockwise (open), the middle is clockwise (closed), and the bottom is counter clockwise(open). This should close off the bypass system and allow full flow of water through the water heater.
If the flush and bypass check don't do the job, you may have a problem with the heater control board. While your dealer cleaned out your burner to eliminate the sooting problem, he probably didn't let it run long enough to verify that the water gets hot enough. Initial run time of the heater under cold water conditions may be 15 minutes or longer (dependent upon the temperature of the water).
'04 Classic 30' S.O.,'03 GMC Savana 2500,'14 Honda CTX 700