There is no pilot bearing when using automatics, so if your 1998 had an automatic then there won't be a pilot bearing
The torque converter has to slide in to the bellhousing to line up the pump drive slots and the input shaft splines
You turn the torque converter while pushing it back into bell housing you well feel and SEE it slide back two times
Once torque converter is in all the way it will be fully inside the bellhousing touching or almost touching the bellhousing in the back
Then you can mount transmission to engine
If you accidentally tilt trans forward then redo the seating of torque converter to make sure its still aligned
Yes there is a Block plate between engine and bellhousing, this is to align starter motor with ring gear, and manuals and autos use different block plates in most years
Flex plate does have a front and back, but if it was never removed then no issue there
Long shot is that your input shaft is too long, although I think you could still install it
There were 3 different input shaft lengths over the years for the A4LD/4R and 5R
Image here:
https://s3.amazonaws.com/sonnax-dev/uploads/mercury_image/image/1943/figure4__7_.jpg
You input shaft should only stick out 1" as shown in fig4