Tough to tell. I think that if they are working now, they'll work with a Joomla template as long as it's fairly simple.
You might run into problems with something like a RocketTheme template that makes heavy use of java scripts. Huge potential for conflicts. The fewer you have the better they will work.
Try creating a test site with these scripts and our Bolt Template. That's as simple as you can get. Add extensions one at a time and see if you one causes a failure. At least that's how I would approach it.
Let us know if you get the job and maybe we can help with specific problems.
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