Toyota Repair: Avalon trunk leak, fender wells, toyota avalon

Question
We find a great deal of water in our 1999 Toyota Avalon trunk wheel well whenever it rains, as well as some in the jack stowage well (usually but not always).  The trunk mat does not get very wet at all.  The problem began after we were rear-ended (at low speed) and had to get the rear bumper replaced, with attendant body work.  The body repair facility is having a great deal of trouble finding the leak.  They have had someone get in the trunk and look for seepage, and they did find one leak behind the passenger side rear tail light assembly, but we are still getting water when it rains.  
Do you have any advice?  Also I would like to verify that this is not related to the original Toyota design, i.e., no Technical Service Bulletin information exists regarding a leaking trunk in Avalons.

Answer
Make sure that the rubber plugs underneath the spare tire and in the fender wells are installed.
Make sure the seal around the trunk is good and that the water can drain out next to the seal out of the bottom of the trunk lid.
There is also a possibility that the water is getting in past the rear window seal.