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Yes, any updates to core components are a good idea, so update Setpatch, FFS etc. (though really you should use a different file system entirely). Things like FBlit and FText will speed up your graphics operations by using the CPU and fast RAM instead of the blitter and chip RAM, though I don't know if the difference is worth it on an A4000 with only motherboard fast RAM.
If you have a wheel mouse (and an adaptor that supports them), install FreeWheel to let you use the wheel in any window.
Personally, one of the first things I do on a new install is move ClickToFront and Exchange to WBStartup and set ClickToFront to work on a double click.
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