There are many templates changes required for things to work properly when upgrading from 3.0 to 3.6 (or even 3.5, for that matter). There were a lot of fundamental changes. The crashes were probably a result of the new JavaScript framework being used, IE doesn't particularly play nice with JS errors.
My advice would be to use the vBulletin default style and make your customisations to that. You're most likely to miss things and mess more things up by trying to make the changes to a style designed for 3.0.
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