Yes, flush and wash the what you can. There are enough pockets of oil you"ll want to clean it out so you do not contaminate the new oil.
Also, I would suggest pulling both side inspection plates and perhaps the PTO to help provide access to clean stuff out. I"d say also pull the shift cover plate too, but you say you have a TE, so dismantling half the front end to do it is not worth the effort.
I wrote a procedure for this several years ago.
I was able to find it here. Link to Oil Change Procedure
Jeff This post was edited by Jeff-oh at 03:23:41 05/11/13.