I have not run this yet, although I have read through it as I was planning on running it.
Initially you should note that the clues in each section are supposed to help move the players along the paths...now if your players are as clueless as mine tend to be you can expand these.
The initial clues that you can distribute point the kids to the farm and the lodge, but I would probably create a scene that introduces one of the clues that points to the farm. (keeping it linear and simple)
From the farm I might concoct something (like a dog or cat food bowl) that indicates there should be one of these around, and maybe have the kids see something moving in the woods nearby. If they investigate they then travel from Wasby towards the lodge.
If that fails, you can also have a character start a scene or you start a scene where they find clue #3 or #4...or simply overhear some kids at school telling tall tales.
The storm can happen any time you want. it specifically says to bring it up after a long day or school and investigating...but it can happen to prevent school (depending upon how the kids are positioned in age and/or if they walk/ride bikes to school) and during the storm (or as it ends) lightning flashes and hits a specific place on the shore (or lights up an area of the water) pointing the kids to the lake again.
Additionally, you can always have a scene where someone says something about it (like a news report or overheard conversation of a parent) that something weird has been seen in or around the lake. this should draw the kids back to the lake for the clues that point to the boathouse to occur.
Then finally once in the boathouse the parts look like junk from the junkyard.
Hope this helps (I will probably use most of these when I run it as well...or if you come up with something better...let me know)