The pic below shows a bearing installed correctly. Note the clip that prevents it from moving out and damaging your seal.
You can't look at the tapered bearings and assume they are hitting something without the case together. I see no witness marks in your pics of those bearings hitting anything.
The seal can be installed in your case from the outside as yours doesn't have a lip on the outside like some of the others do.
If it were my car, I would just pull that needle bearing out and run the tranny without it. That bearing is totally useless when the t-case is in the car as the t-case coupler has tapered bearings in it to hold the shaft. The only time the needle bearing is in use is to hold the output shaft in place better when the t-case is off or if the t-case coupler/bearings have a failure of some kind.
Jack