You can select what Migration Assistant will move.
Do not import system or network settings or apps
Just use Migration Assistant to import your personal data.
Do not delete anything from the Mac Pro until you are happy
everything is working as you would like it on the Mac Mini.
2008 Mac Pro, graphics card easily replaced, quite easy to get other parts for it, maybe just needs a good clear out,
dismantled as much as you can and rebuild. I have clothed my entire family with the dust this thing collects.
My 2008 MP is still going strong, 13 years old in March.
Replaced a DVD drive and upgraded the graphics card, installed two SSD Drives and upgraded two HDDs,
If this thing ever pegs it I am going back to running about with sticks and making fire.
And yes "officially" it can't upgrade further.