You could try to add the new theme as a Child Style under the (Parent) Style that you added your hacks in. Then in your Parent Style update all of your templates that you've added your hacks in by pressing "Save". By pressing "Save" your new theme should inherit whatever edits you've made in the Parent Style.
I think then in your Plugin System --> Plugin Manager at the bottom click "Save Active Status".
I haven't tried it so I could be way off the mark.
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