[dsraven]

before you start check availability of the required gaskets in a neoprene style for the pan, possibly a new front sels since it will have been disturbed a few times and they don't usually like that, pick up a small tube of "the right stuff" for the dabs in the corners, and then take it apart. before you install the pan get yourself some longer bolts the same size as the pan bolts and cut the heads off them, hacksaw a groove in the cut off end for a screwdriver to fit into and screw them into the 4 corners of the block so the pan can be slipped over them for good alignment. sometimes I use a stud actually so a nut can be screwed onto the end and the pan can hang there just below the gasket while you make sure everything is good first before pushing it up the last little bit. also, place the pan on a flat surface and use the round end of a ball pein hammer to sit over the bolt holes, then strike that gently with another hammer so the distroted area where the bolts have been sucked up can be made flat or slightly convex the other way. this helps to not cut the gasket in that area when the bolts are torqued down. I also use weatherstrip adhesive on the rubber end gaskets to hold them in place as i find the silicones and other liquid gasket type materials only seem to grease things up really good and then you never really know if the rubber part is intack or if it has squeezed out the one side or the other. it is like contact cement so it almost dries then you install it and the part stays put. some "right stuff" in the corners and good to go. sometimes I use the aviation form a gasket stuff along the block rails to hold those gaskets in place, it never really dries dut holds the gaskets pretty well for alignment, espcially if you have a few studs placed along to hold things where they should be.
LG could be exactly correct with his theory on your bolt holes. if you drilled or tapped the holes there is likely a burr on the inner edges of the flat steel part that is always left behind during these processes. it is likely not allowing the 2 parts to sit down flush against themselves.
when you get after it post up some pics of the leak found and also the tear down and repair. there is always somebody looking, now or later, that has the same questions or problems.