When I upgraded my pc:-
I have SH5 on disk. Now due to ubisofts wonderful online reg

I no longer need the disk. All I have to do is sigh into Ubi launcher and my registered game is there to download anytime I want.
So Game state as it is (Mods and saves)
Mods
Copy your mod folder to your external drive
Saves
Allow online saves
Upgrading you PC
Save your mod list snapshot file to your ext drive.
Replace your PC
Download game from Ubisoft (you can download as many times as you want as long as you are signed in)
Update to v1.2
Copy your mod folder into your game file
Run JSGME using the saved snapshot
Load and run game - online save will reinstall
Continue where you left off