A lot of guys like to use RTV for the front and rear lower seals - if you do that, make sure you let it set up and get a little stiff before you install the lower. Either go that way, or I got the intake-to-head gasket kit w/ the rubber end seals instead of cork. Most of us agree the cork gaskets don't work very well.
Michael Yount once posted this to help me and I try to post it in threads like these:
To get the lower lined up correctly, which can be difficult at times, get some bolts the same size as the lower intake bolts (should be 7/16) about 2 inches long, cut (or grind) the heads of the bolts off, slot them and use them as dowels or studs to help line up and properly install the lower. One on each corner should be fine - so 4 total. Once installed and you get a few bolts in, remove the dowels w/ a flat head screwdriver and put your bolts in. Remember to follow your torque sequences and amounts in your manual.
I don't know if it comes w/ gaskets or not, but a stock uppper-to-lower gasket will not work because the ports are different. You can get the gaskets from summitracing.com (about $20 for 5 gaskets) or an auto parts store. If they don't have 93 cobra gaskets, you could probably get one for a 96 explorer and it should work I believe.