Furnace cycling (Limiting) is caused by:
Restricted or insufficient discharge ducting
a. Ducting must meet furnace’s minimum requirements.(Not enough ducts)
b. No excess ducting or unnecessary bends. (Duct could be crushed...should check each duct for amount of air flow......low air flow should be checked for obstruction in that duct)
c. All closeable registers must be fully open and unrestricted.
Restricted return air supply
Make sure nothing is blocking return air on furnace cabinet
Defective limit switch
Replace limit switch
Overfiring......propane pressure set too high.
Should be 11" WC with at least 50% of other propane appliances in service (ALL of them is better)
I'd be more concerned with the water intrusion.......water can cause extensive unseen damage.