Here are my impressions =>
1) If you have a milky white / pink transmission fluid then there is probably water contamination. You need to confirm this ASAP because if you have a way of returning the transmission you have just fitted and getting your money back do so.
Water in a transmission causes dreadful damage.
If you want to see pictures of water damage in a 722.303 have a look at the pictures in this thread
http://www.peachparts.com/shopforum/diesel-discussion/323259-722-303-bits-photo-shoot.html
2) Vibration could be something as "simple" as a poorly aligned prop shaft - did you match up the marks? - but with water in a transmission it could be rusted bearings - it could almost be anything corrosion related in there - nightmare.
3) As for transmission flushes - I'm one of the few here of the opinion that a "flush" is really a placebo effect for an anxious owner...
...I mean a flush must be better than a simple fluid change right? Bollocks! There's no way a flush will remove years of grit grime and **** from a valve body / actuator - hydraulic systems are not high flow systems - how can it flush? Where will it flush to? (Take a look at the pictures in the thread linked above and tell me where it all goes if you don't believe me)