I was hoping to simply connect the motherboard to the internal motherboard and then desoldering the ports and add wires so they could match up with the SE ports.
To keep the hack within the realm of possibility:
00) do your mod in reversible, if somewhat
over the top, steps
01) make your wires long enough to slide the Shell back about 6-12"
02) mount all your extra ports through the SE's Expansion Slot Opening and an extra battery cover
03) definitely use a single slot riser for a USB/Firewire Card
04) mount the PSU (6360 or ATXhack) vertically on the back of the shell & rewire the AC to the original SE Connector
05) hack the shell so it slides back said 6" without much effort
06) use an external monitor at 640x480 for Tuner Card Output set up right next to the SE/6400
07) add a shallow MacQuarium with a single Siamese Fighting Fish to replace the CRT for the nonce
08) slide shell back to feed your fish and lift the tank out for maintenance.
09) mount your filter, aeration device next to the PSU on the back wall
10) fab a catch-basin to surround ALL the MacQuarium parts in case of leakage
10) mount a tiny WebCam w/closeup lens to the backside of the "catchbasin"
11) feed the output of the WebCAM to the Video Card
12) output the rear view image of the MacQuarium's Siamese Denizen to "spanned" monitor
13) along with the face of anybody staring into the SE/6400!
In doing so, you'll have a fully functional SE/6400/MacQuarium with modern I/O, FDD and (second) Monitor! [

] ]'>
You'll not have modified
ANY of the SE's external parts and your CRT/Analog Board will be safely stored away until you source a GrayScale CRT or LCD! You'll have lots of time to consider options while having done a really cool hack already . . .
. . . one which may satisfy you in itself! }
p.s. hacking your wiring to an EdgeCard Connector/Slot PCB set for your wiring harness makes things MUCH easier & gains bonus

points!
edit: Now
I'm tempted to do this friggin'
WhackHack! :