1) The assumption is that Trump intended to purposefully do something improper... which may not have been the case. Regardless of what happened, clearing the room of those particular people does NOT show intent to do something improper. Those people should NOT be in the room during any discussion of the investigation, regardless. Clearing the room doesn't indicate intent of impropriety. In particular, failing to clear the room for a discussion about the investigation would definitely have been improper.
2) You're also working from the assumption that Trump's comment was impossible to be anything other than a direct order to stop the investigation. Comey interpreted it as a request to drop that investigation... but Comey's interpretation is not necessarily reality. Likely, yes, but not definitive. It is plausible that Trump did not intend it as an order. I don't think that's likely, personally, but I think any half-way decent lawyer can easily make that case. Unless the jury has ESP, there's no clear way to know. And given that Trump did not take any other actions to impede to halt the investigation, I think you're going to have a hard time proving that intent.
3) There is no need to prove (or even suggest) that Comey lied about anything at all. Comey's testimony can be 100% accurate. At the moment, I'm inclined to view it as accurate. But the accuracy of Comey's statement is irrelevant to your interpretation of that information. Comey wrote a memo about a meeting he had with Trump, where he felt that it might have been an improper request. "He wrote a memo about it!" doesn't make it obstruction. "I felt like he might have been asking me to do something improper, but I'm not certain" doesn't make it obstruction.
4) Comey seemingly contradicts himself on this point. Read the testimony. At one point he says that no, he didn't think Trump was asking him to stop the investigation... then at a later point following a leading question he said that he felt it might have been an attempt to pressure him to drop the investigation, but wasn't certain.