My hunch is that simple copy/paste should work. However, the safe procedure is to start from clean of course. This also gives you a chance to get all the lastest versions in case you missed some updates.
Why not copy/ paste a few minor mods and see if those work alright? If they do, the others should be the same as the working scheme of all mods is the same (.esm/.esp's looking for resources, all is happening in the /data/ folder). I'd be inclined to be optimistic here.
I would in any case install the tools afresh, not sure if WB and OBMM will work when you just copy/ paste their files and directories (because of registry entries and so on)...