First off, welcome to the site. I trust you had the opportunity to read the 4R70W rebuild Diary to the point it's at (I will finish it when it cools down and i can work in my garage after work... too hot this summer plus vacation, etc.).
Let's start with the scarf cut seals on the output shaft. Millions of vehicles have done just fine with them. They are not AS good as solids, but you are NOT making a HORRENDOUS error by using them. I try and include ALL upgrades in the Diaries so people can see what is out there. Make sure there are not any burrs or anything in the grooves for them.
The stub shaft interconnect between the direct and forward. This goes pretty deep into the forward, so relax there. Spline damage is mostly what you are looking for. Into the Direct the thing you are looking for is slop... if you are suspecting the direct drum you MIGHT want to consider replacing it with new.... about $70
The two holes in the output shaft... one is plugged and was a machining hole. The other is a feed for lubrication, and has a plug lower on the shaft bored to about .050. Not much oil pressure coming though there.
I don;t have a direct drum easily accessible (in the garage rafters and it is HOT) but even if the stub rested on the output I do not think it would be a problem.
It sounds like you have done well, and identified problem areas. Those steel sealing rings are a problem child. Speaking of which do you want to sell your old damaged case? I can resleeve the output shaft bore.
Anyway You are doing well grasshopper. Let us know how the rest of it goes! If you have any more questions, why not start a new thread where more people will see it? Or post here:
http://www.explorerforum.com/forums/showthread.php?t=161450
As in many things, there are more and more "subject matter" experts on here as more and more people delve into their own auto trannies!
ps. I am willing to put solid seals on that output shaft for ya... via round trip mail.