Don't. You'll never get them aligned again.
If you think those bearings and seals are shot, rebuild a used eBay supercharger with good bearings in the intermediate plate.
Or consider a replacement set of rotors pre-mounted from www.canadiansupercharger.com
Needle bearings and nosedrive rebuilding is as far as you should go on your own. Doing what you propose is impossible without a factory alignment jig to pre-set the backlash in the rotors and gears while the gears are pressed back on.