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If you move the Windows taskbar to the other monitor, DisplayFusion will then create a taskbar on the main monitor. Then you can right-click the DisplayFusion taskbar on the main monitor and use the Multi-Monitor sub-menu to disable the System Tray/Clock, to clear up the right side of it. That will still allow you to have taskbars on both monitors and show buttons for the programs on each monitor. Will that work for you?
Regarding the transparency, you can sort of adjust this on the DisplayFusion Settings > Taskbar tab, though it will be difficult to get it to exactly match the Windows taskbar.
Hope that helps! If I misunderstood any of your requests, please let me know
Thanks!