On board SCSI? That sounds like the Z3 board. If it is, forget the PowerFlyer and get a Cyberstorm for the accelerator slot. That's got SCSI-3. Or use the SCSI on the bus itself, it'll definitely be faster than the internal IDE port.
The Micronik board is annoying. It obscures the entire motherboard. I don't know what can fit, but even clockport peripherals would probably be a squeeze. I'd say there's about an inch clearance, probably less. You'd definitely want some insulation between the boards. I don't own a PowerFlyer myself, so I don't know how large it is.
Yes, it probably could go in a Power Tower. Before the Z4 board came out, Power Computing were selling Power Towers with Micronik Z2 boards. If you have a Z3, it should fit, but I'm not certain.
If you do swap it into a Power Tower, I might be willing to buy the Micronik case. I need parts for mine. :hammer: