A well-engineered ram-air intake from the bumper should have a dip in it with a drain point so that all water splashing through the tube gets collected and drained. A long vertical section over the dip on the engine side is best, since very little water can get sucked all the way up, even when it is at WOT and heavy rain is coming in. However, the fenderwell air is cold and protected from the elements pretty well, so the airbox works well. To seal the top of the heatshield, try the closed-cell foam they put around pipes. You can find it at Lowes or Home Depot.
