I movt
The main thing I noticed is your transition at 2:00 came just in time to save the listener, good timing.
From your description, I think you accomplished your intent of a baroque/classical mix. I couldn't tell about the organ clashing, but i think you could use some more relief, more without organ (and in the third movt especially, but it might sound better with a real organ, it's presence was very unwelcome in the third movt), it was overall too constant for my taste in the first. But keep in mind my taste is not friends at all with the classical period, and although I like Baroque better (especially Bach), it's not my thing either. So I'm saying what I liked instead of suggesting very much.
II movt.
1:15-1:35 is my favorite. At 1:27 I was afraid it was going to belt out the tonic over and over from that point on, then the chord at 1:32 was amazing.
III movt.
Other than the organ comment, I would say congratulations on writing a fugue. It wasn't very adventurous, and yet it kept the overall mood of the whole work. Maybe that's what you wanted. There might be a way you could look into orchestrating it differently so the different voices/entrances etc. are more easily heard. If you hadn't said it, I'm not sure I would have picked up on it being a fugue. Maybe you want that, but as cool as fugues CAN be and as difficult as they are to write, I think you should make the voices more distinct, which would also add a nice contrast to the sinf. as a whole.
This does sound like fun. Good work.