just installed the Android Market and it's working fine apart from one thing: a lot of applications seem to be missing
You should expect a number of apps to be unavailable (not really missing), because for instance there may be some minor incompatibility with Gingerbread which the developer didn't want you to damage his rating for. For instance I can sideload some Froyo games where the controls are crossed up under Gingerbread.
But if you see a massive lack of apps, I wonder if you used one of the rooted approaches to install market. I saw reports in the associated forums of intermittent problems like that. It's hard to follow, but I saw even the author of the latest approach (finless) report that once in a while his installation of latest 1.3 firmware would do this for him until he reinstalled. (EDIT: now his installation page describes some other solution involving deleting files)