I pulled mine separately, but when I separated the tranny from the T-case the tranny output shaft pulled forward and dropped the needle berarings into the tranny. i didnt notice until i had the tranny back in and the T-case wouldnt mount up %) . so I had to pull it again, and put the bearings back in. it was much easier lining it up the second time
one thing i also did was group the bolts into separate, labelled zip-loc bags -- "Bellhousing to block", "fly wheel to crank", "t-case to tranny", etc. it saves a lot of grief, especially if you need to pause for a week or two when life gets in the way of wrenching.