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This is a tricky part when converting HTML themes to react. If you are using jquery to manipulate DOM then you are neglecting the core principle of react. I have been through same situation few times. I have tried custom.js method you mentioned. From my experience it's not worth it you would run into lots of trouble and end up writing half of the libraries. And don't get me started on production you will want to rewrite everything from scratch.

I would suggest you to use equivalent React Components. It will be much easier for you to maintain the project later.

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