The problem with the approach you have choosen is that on my DR the settings for the Recent Files patch and the binding of xournal files would be lost, since you are replacing gconf with a different version. If more people start sending updates with this mechanism, only one update can be active.
Did you look at the update/restore-script that came with the 'evince file-extension' patch? They might be sufficient for your patch also (with a small modification). Maybe for your next update?
W.r.t. the mobipocket plugin did you already see the problems in the emulator or only on the actual device?
Thanks Very Much for creating this viewer and sharing it with us.
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