Newb Q: How to format&reinstall everything correctly (mac)

I have been using cubase for quite a long time, but i have only recently swapped my trusty Windows PC with a Retina Macbook Pro.

Now after updating to Yosemite, the battery life has gotten impossible to deal with, and the whole thing became rather sluggish (top-spec 15" rMBP), so i was thinking about completely wiping it and reinstalling Yosemite freshly.

Now i have a 4TB ext. HDD with a 1TB time machine-only partition, which is already set and backed up. But i also have a lot of free space which could be used to make a complete copy of the internal SSD, with all data and its locations preserved.

I’m just scared now that when reinstalling Cubase (pro8) and the plugins, my projects won’t load, or they will not be able to load the samples I used on this current install.

What would the best route to choose? There’s seemingly a “reinstall” option that keeps all data intact, but i’d much rather start fresh because of the problems i’ve been having with Yosemite.

So, can anyone please help me?