I know you read over the posts in the following similar thread, because you posted there too: 4L60e - Endplay issues
Anyway, I just happen right now to have a partially assembled trans with only the pump removed. It has a tight 0.015" of endplay. I put a straightedge over the case tabs that bolt to the pump. I then measured exactly 0.125" of space between this line and the top of the reverse drum. In other words there is 0.125" of space between the reverse drum and the pump; a plastic washer takes up most of that.
Also, with the pump off, I can lift the input shaft about 0.050 before it starts to lift the reverse drum.
This might help you determine where your problem is. If your reverse drum is sitting much (e.g. 1/4") lower than mine, then your sun shell is likely sitting too low.
If the reverse drum is in the correct position, then your input drum is sitting too low, perhaps due to something missing in the front planetary.
Sorry, I don't have enough experience to pinpoint your problem, but perhaps that helps. Also, did you replace any hard parts?