Thanks for the useful picture and PDF plan. It looks as if your rectangular inlet pipe extends right down to the baffle plate and I wonder how far is the end of the outlet pipe from the baffle? Very tidy build did you use bendy MDF for the side wall?
Have you tried having a longer section of rectangular duct between the transition and the top hat? Perhaps 12" to 24" long. It should ensure that the flow in is less turbulent. I would like to know if this reduced turbulence improved separation or otherwise. Perhaps it works well enough for you not to need to do any more experiments but I am hoping you are as inquisitive as I am. Regards from Wessex.
Have you tried having a longer section of rectangular duct between the transition and the top hat? Perhaps 12" to 24" long. It should ensure that the flow in is less turbulent. I would like to know if this reduced turbulence improved separation or otherwise. Perhaps it works well enough for you not to need to do any more experiments but I am hoping you are as inquisitive as I am. Regards from Wessex.