There's one more (actually 2 more) parts that you might be missing. They also might be present on your old cover, so you can reuse them from there if you have them. There are two small sleeves that fit into the bottom two bolt holes in the timing cover and protrude towards the block a little bit. When the cover's installed, these sleeves fit into the bolt holes in the block. Their purpose is to correctly locate the timing cover on the front of the block so that the front seal around the harmonic balancer is centered. If the cover is not centered properly, then this seal can leak - or start leaking very soon due to it not being centered around the balancer hub.
Butler (and others) have them. Butler's part number is APE-N538S.
You can see them installed in a block and where they go in this photo:
0208Hpp Running16 Zoom Photo 17