Looks good.
As for the tranny what I've always done is balance just the tranny on the jack and get it bolted up into place. Then add the crawl box, then the t-case. This way you have the least amount of weight to deal with. Of course a tranny jack really helps too, or you could make something out of square tubing that fits on top of your floor jack and holds the tranny in place. That's what I did before getting a tranny jack. May still have it laying around. I'll check and take some pics if I do. FYI, if needed to you can usually rent one for about $35 per day.
As for the shifter plate I just made a separate plate for the third shifter, but I think the full plate for all three would look a lot better, so go with it. I plan to do that with mine some day, but I want to lower the hump and also make it removeable first.