Right now I'm playing an original 1996 Fender Jagstang. I'm not sure whether or not its a good idea to switch out the original parts for new ones. What I'd be looking to change is getting some locking tuners, and swapping out the pick ups. I don't know if this will "decrease its value" or anything like that, since its a limited edition guitar. I don't have any plans to sell it, but I just don't know what to do in this situation.

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Since you have no intentions on selling it, then mod away.

Most guitars aren't considered very collectable and so modding isn't going to really affect its value. But if you're really paranoid, just do mods to the guitar that are reversible i.e no structural modifications made. Replacing pickups is completely fine provided you provide the originals when you sell on. New tuners should be fine provided you don't have to drill any new holes etc.
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I also have to do that. Cottaging this weekend