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It seems to me you are looking for some magical conversion tool that will take a crappy input and produce a clean and easy-to-convert output. Unfortunately, there is no such tool. All converters try to handle such a situation, but the results are mixed and usually much worse than you would get by hand-editing. Sure, hand-editing is a lot of work and needs a lot of knowledge, but it can be done and once you try it a few times, the process is quite easy and straightforward. Unfortunately, it is not something that could be summarized into "replace A with B" list - a lot of the necessary steps are done in a "I look at it and see the solution right" way.
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