Hi Simen,
At least YCF is for some slightly useful purpose to period composers. It works great for posting music on.
Regarding your piece I really like the overall sound you've got going for a lot of it. My first suggestion would be again to create a score that has nothing to do with what you needed to make the mp3 sequence play correctly. So for example get rid of having BOTH a cello AND a continuo part since they're the same music! Your 6 page score will then probably fit on 2 or 3 pages and be much clearer to read.
Your opening themes sound nice but right off the bat you kind of shot yourself in the foot (hopefully all these American slang terms work for you!) because right in the 2nd measure you end up with parallel octaves between the cont. and the flute where they both go from A to F#. I think you could easily fix it though by just having the bassline play a D rather than the F# in meas. 3 so that your bassline would read, D-E-F#-G -F#-G in 16ths. And though that immediately changes your theme I think looking ahead it will work for the flute too...
Looking ahead to meas. 14 you don't avoid a parallel octave there either just because the flute part has a passing D between the E and the C# just like the bass does
After that my attention span for looking for errors starts to wane.
At the final cadence however I'd suggest 2 things, First you really almost always in baroque need to set up a nice official IV V I kind of cadence with your bassline. The bass going up to the C# is probably going to come off sounding weak. Also I'd get rid of the odd rhythm you have the flute doing at the cadence. There's no precedent for it anywhere else in the piece that I see. Also timing-wise I'd strongly consider trying to get your ending to end on beat 1 of a measure rather than beat 3.
And FINALLY
If I were you I'd strongly consider transposing the entire piece up by maybe a 3rd or 4th. "C" technically is the lowest note on a flute but that doesn't mean they want to dwell playing way down there that much. And in reality you'll barely be able to hear the flute that low. Why don't you see how it looks being in F or G rather than D?
