Before you act on Sailor Steve's advise (re: remove old game folders), please consider this: In the old MODS folder sits JSGME.ini, which is just a text file to help JSGME remember which mods are applied. This could be used by you to make a list of which mods you need, and re-assemble the mod-order. You can open it with Windows Notepad for example.
Since you experience game crashes you might have mod-corruptions, so I strongly advise against re-using the other mod folders inside it.
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