With separate parts you get 3 times more detailed textures and usually 3 times detailed solutions. For our purpose we scanned character in T-pose and posed/animated them later.
What i did (if time permited) was:
For legs parts have chracter wear only pants and boots to get proper deformation over boots and shirt tucked inside pants for easier masking out mesh. Shoot this with legs only visible in images (you can zoom in to get large cover). For this i have rotated cameras vertically to get more coverage.
For torso parts have character wearing what you want and placed over pants as you want to be. Zoom in as much as possible to get full frame of torso part (head doesnt have to be in frames). For this part i have rotated cameras horizontally.
For head i had character wearing gray shirt (something like this:
http://wpecdn.com/media/catalog/product/cache/1/image/400x/9df78eab33525d08d6e5fb8d27136e95/i/m/image_64592.jpg which have noise pattern and that helped PS aligning points) and camo beanie like this one:
http://www.nexternal.com/armynavy/images/Woodland-Camo-Beanie-Watch-1.gif if you dont need hair. Those two helped getting alot points and compesate for oilness of skin and hair when aligning cameras and finding points.
For full body pose it as you want wearing same clothes as in separate sessions and align photos. The purpose of this solution to get locations where shoulders, head, waist are and proportions so you can place your separate solutions in same locations.
For full body and separate parts i create final high poly meshes and very low poly mesh (~20 k) for easier manipulation. I use Modo for aligning parts (you can use any 3d app) . You can move loaded meshes in "item" mode around virtual scene. This means actual position of vertices and polygons arent changed only handle so when you replace low poly meshes with high poly you get position, rotation and scale correct.
Sory about crap explanation of workflow
, hope it helps.
Admir