Just for my own observations, are you using the Notepad method of manual targeting or what the SH3 Community Manual calls
"Full Manual TDC" (bottom of page), where you completely ignore the notepad and manually calculate range, speed and AoB using the navigation chart?
I prefer the second one because it has the advantage of working better in rough seas as well as the fact you don't really have to identify the target completely to get a good solution (though it does help for determining spread angle and running depth).
Plus it feels more "manual" to me, though since it relies on the "God's Eye View" setting left on, I'm not really sure which is more realistic. I suppose the truth is somewhere between both methods.