Font Alignment Help

We designed a complete font (regular, bold, bold italic, italic) based on classic "Font X" Opentype standard, otf. The result was a one to one match on spacing/decent/ascent.

Now we are encountering that Font X itself, does not match it's own TTF font.

We don't know if this is because the OpenType Std has only 253 characters, so it's not matching the TTF which has a full set of 2000+?
Or is it because OpenType Std is at 1000UPM versus TTF at 2048UPM? Even if we convert the OTF to TTF at 2048, and match the exact same settings, it fails to align.

For testing, we must use TextEdit on the Mac. The following problems occur:
Major misalignment happens in leading at point size 8, 9, 10, 11.
Small amount of shifting happens in point sizes 12 and up.

To test on the PC, we must use WordPad and NotePad.
Major shifting, leading and big problems in kerning happen at all point sizes.

We have not been able to adjust the settings to achieve alignment.
Some of the settings we have tried and could use help understanding are the following:

UPM: 1000/2048
General: Ascent/Descent
OS/2, Metrics:
Win Ascent Offset
Win Descent Offset
Typo Ascent Offset
Typo Descent Offset
Typo Line Gap
HHead Ascent Offset
HHead Descent Offset
HHead Line Gap

We need a Font Lab genius, that can guide us through the settings that can solve our issues. Thank you!