Hi, I'm just a new user who could not care less about the quality of my little Khmer community on Wikipedia. Fortunately, I happened to come across your page and this is one of many issue on Khmer script on site! with my understanding of the language, I would like lend you a hand on this one:
(Pardon if I'm coming out as being rude; I taught myself English.)
??? : The subscript for ត and ដ are identical (almost); there are no rule for the order since they cannot be used on the same consonant.
from the context; the subscript of ត(្ត) are grammatically used (ស្តា : ស + ្ត + ា), though you can use ដ(្ដ) with the same effect (ស្ដា : ស + ្ដ + ា).
Syllable boundary errors: The original កុំែ ( ក + ុ + ំ + ែ ) is in correct order, កុែំ ( ក + ុ + ែ + ំ ) is not. The same goes for the other involve ុំ(ុ + ំ), ុះ (ុ + ះ) and េះ(េ + ះ), using the order as above. (the context are full of grammatical typos)
Another one is ពា្ឈ ( ព + ា + ្ឈ ). From the grammatical standpoint, that is certainly incorrect, but I think the author are using it to achieve this effect: ញ + ្ឈ = ញ្ឈ . The possible explanation is Khmer Unicode wasn't fully developed back then, so the writer had to substitute it with ព+ ា = ពា .
ច៎ា ( ច + ៎ + ា ) is the correct one. ៎ is used to emphasize the sound of ច to make it sound more short and sharp, so the reorder one is incorrect.
That is all that I can help for now. And thanks for your hard works!
(P.S. half of the the sample you're using are broken beyond recognition; common reordering won't make them readable)