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Sorry if I'm not understanding your question completely but when I replaced my top with a glass window version it will definitely not raise up as far as the plastic window. This does limit access somewhat and makes it a little more of a challenge to work on but it will still raise up.
I recently lost my transmission gears and converted it to manual operation until I can get around to replacing them but I can still get the top in service mode. I don't know of anything that would restrict your ability to raise the window just because you removed the rod linkage.
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