The main issue is to get things to look good, I've seen too many conversions that looks to be done with a hacksaw and with a timelimit of about 5 minutes.
Some of the imediat issues and ideas on how to solve them.
External keyboard, it's not as easy as with the A500 with just some soldering of a port with wires to the MB, but in fact needs some hardware such as the EZ key.
Room/cooling for a turboboard, can easily be solved with extra long mb distances... especialy if you calculate with this from the beginning of the project.
PCMCIA port. Do you want it sticking out of your tower or do you want it internaly only. If you want it sticking out I suggest giving 2-3 cm clearens between the mb and the chassi side so the card doesn't have to stick out as much (also make the hole a bit bigger as some amiga pcmcia devices doesn't follow the size standard), if you want it internaly it can be closer to the MB side if u use an pcmcia angle. Internaly will be great if you only intend to use it for a NIC. Have you intensions of using more things with it (PCMCIA2CF converter, SquirrelSCSI etc) then external is the only way.
Power supply. The A1200 powersupply is very weak so a nice PC PSU is recomended. How do you want to add this power to the MB, easiest is to hack on the A1200 MB connector to the PSU and have it connect to the mb. If you have the mb right up next to the back of the chassi this meens the cable need to go outside the chassi (not cool). Then it's better to solder on a MB connector from a PC right onto the Amiga MB. That way the powercable can be cept inside and the PSU doesn't need to be hacked. Also you don't have to make a hole on the back for he power connector (looks better).
Buttons and leds. Power button can go stright to the PSU. Reset button can be connected to pin 9 and 10 on TP1 (suggest soldering a jumper header on the MB). Leds goes to the mb jumpers for leds, make a little trint with 2 jumper headers and make room for a resistor to each led or they will pop within weeks.

The rest is pritty stright forward, all you realy need apart from this is longer cables for IDE and floppy.
Ow and with a desktop you now realy have room for all those nice internal hardware addons and room for fans to cool things down propperly.
