So here's my tutorial of sorts, in case someone else is making one of these.
The Boat:
-It has to be as light as humanly possible. Minimize weight and maximize the bottom surface area. This means little to no K'nex pieces. I made mine with pieces of tagboard wrapped in duct tape.
-There must be wheels in the bottom, but they must be small and turn easily. Lego wheels worked best for me. I hot glued them to the bottom of the boats.
-Finally, place pennies or some small weight near the back of the boat. This allows for the current to push the boat easier.
The Trough:
-Width: I used yellow/granite rods for the trough. This size should be most consistent with the Screamin' Serpent coaster size.
-Height: I overestimated how high this needed to be. Anything over a blue rod in height (2.25") is probably too much.
-Waterproofing: Sorry, but nothing is going to be absolutely waterproof unless you get custom designed plastic or cut pipes from Home Depot in half. I personally got tag board, wrapped it in duct tape, and then added another layer of duct tape when piecing it together in the K'nex trough structure.
*Side note: FlexSeal does not work. At all. It smells bad,t akes forever to dry, and does not waterproof as good as duct tape.
Water Depth:
-This is a tricky one. Water must be AT LEAST deep enough for the boat to float. But not TOO DEEP that the water velocity drops and the boat gets stuck.
-Before a drop: Just before any drop, the bottom of the trough must gradually rise just enough for the wheels to roll on the bottom. This allows the boat to fully float before the trough, and gives it just enough propulsion to push it onto the drop portion.
Lifthill:
-There's a million viable options here, but the easiest is to use coaster track with pieces attached to the chain to pull it up.
-Make sure the beginning of the chain is much lower (and begins much earlier) than the end of the trough. Also, make sure the end of the trough has a lip to maintain water depth - sort of like before a drop.
Other tips:
-Smoothing the sides of turns is very important. This is where the boats like to get stuck. This is actually what forced me to make them boats - not logs. I ended up lubricating the sides of the boats and trough with beeswax from Lowes to make sure I didn't have to deal with the problem anymore.
-Make sure you build this over some sort of a pool, or catch tray, or something. I don't recommend you make a flume ride indoors until the design gets more perfected.
-A 500 gallon per hour pump should give you the flow rate necessary to propel the boats. It costs ~$50. But if you can functionally lower the water level in the trough, you should be able to get away with a cheaper pump with a lower flow rate.