EzKey from Elbox is a nice hardware that lets you attach a keyboard port on the internal keyboard connector. There are several others too... some that takes Amiga keyboards, some takes PC keyboards... some take both as the EzKey.
The scanmagic is a scandoubler flicker fixer that exist both in an external and internal version. I suggest you go for the internal version... it will fit inside a standard desctop also so don't worry about that.
Depending on how you place the motherboard and how big a tower you get (bigger is almost always better) the PCMCIA port can be blocket but there are hardware that turn the PCMCIA 90 degrees.
There's an obvious problem being how to power the Amiga. In my A1200 tower, to avoid external power whires, I soldered whires directly on the motherboard to a connector that the PSU power connector for motherboards then went into. AT PSU are easiest to convert but ATX will also work.
Another thing to consider is to make sure there's room for possible uppgrades further down the road such as a MediatorPCI or other bussboard solusion and a turboboard.
