I'm quite experienced in vb-integration projects. Here is my advice:
Shape your new user db design so that it will use vb's default design from now on. It's always much more easier to adapt third party user database to use vbulletin user database instead of doing otherwise.. So convert your users/passwords to vb and from now on use vb database in your entire site. I wouldnt recommend hacking vb to force it use another login scheme of another software, it will be time consuming and awkard. In most cases it's easier to forget about your third party software and use/code an alternative of that if necessary..
My 2 cents..
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