Let's see. Well regarding M.4 I don't see any major issues but:
If you're not sure about 9/8 just change it to another that better suits the phrases you make. Perhaps 2/2 would be worth trying, it does indeed sound to me like 2/2 or 4/4 instead of 9/8 in the very first measures. The use of so many fermatas in the first four measures suggests that 9/8 isn't an adequate choice. Perhaps it is later, but nothing stops you from changing the tempo after the intro.
For your next questions, there are a billion answers. You could use any harmonic progression that came to your mind, you could do a 16-bar bridge between that E chord and the melody at bar 12, hell or it could be 128 bars long! You could just use single notes in the right or the left hand for those two blank measures. Which one from the billions of things you can do is going to work? That's for you to discover, and perhaps what works for you is something I could never have guessed or that I wouldn't have used. The same goes for the harmonization of the bars from bar twelve and so on. There's again a LOT of things you could do: You could just repeat the structure and 8va or a perfect fifth, major or minor third below, you could add entire chords like C+ and F for that very first measure and keep going with that or switch to some ostinato in the left hand... You could NOT harmonize it. But again, since it's your composition it's for you to discover and choose.
And no, it's not a bad thing that you now don't know how to keep going. Let the piece rest and think about it when you be eager to, just don't give up and ideas will certainly come like they did for the passages you have written already. I've briefly gone through your other material; perhaps M(22-27) is suitable to do some kind of bridge between your first measures and M12. If you are really out of ideas or just don't know how to work with the bass, well this is a piano piece so get yourself full of listening piano pieces by every single composer you know and don't know yet.
Finally, don't be afraid of "repeating" sections. If you find something that works, explore and develop it, and perhaps more ideas will come by just that development process.
Sorry if my answers didn't satisfy you, hope you keep trying in any case.
Kind regards ^^!