Alternative to Indirect Questions

Solution 1:

The syntax you want to use doesn't sound natural to me (also a native speaker) for an indirect question. What you seem to be asking is a direct question: I'm wondering, "What is the time?"

This site gives instructions on how to make an indirect question. And this one an explanation of how embedded questions are formed.

Perhaps you could use ellipsis.

In reported speech, the ellipsis is sometimes used to represent an intentional silence, perhaps indicating irritation, dismay, shock or disgust. This definition is more known with younger, internet savvy generations.

or with a different use from the same Wiki page:

The ellipsis is one of the favorite constructions of Internet chat rooms, and it has evolved over the past ten years into a staple of text-messaging. Although an ellipsis is technically complete with three periods (...), its rise in popularity as a "trailing-off" or "silence" indicator, particularly in mid-20th century comic strip and comic book prose writing, has led to expanded uses online. It has been used in new ways online, sometimes at the end of a message "to signal that the rest of the message is forthcoming.

Solution 2:

You want advice? Yes, I have three suggestions for you:

1. Don't overthink it. As Neil Coffey says, you obviously understand the issue and have thought it through. Your problem comes with thinking about it too much and giving yourself over to semantic satiation.
2. Don't let MS Word's grammar checker boss you around. [See Item 1]
3. Any of your examples would serve, with the possible exception of "I am wondering what is the time." You're right in thinking that without punctuation this sounds a little off, or dramatic (given that it may be seen as an example of the rhetorical device known as anastrophe. If I wished to avoid that, I might use a comma ("I am wondering, what is the time?") or a colon ("I am wondering: What is the time?").