Al,
my box is mounted with rubbers at all 4 corners. I'm not sure of the original biscuits that were used, but on mine a close match turned out to be Anchor Industries No. 2009. Its a round biscuit with a bit of a cone shape to one side that works out pretty good with a heavy washer under the mounting bolt head. There is also one on the underside of the crossmembers it attaches to, supported with another washer and a sleeve above the mount ear on the transmission. This gives a rubber sandwich to absorb vibration and cushion in either direction. They are available from several sources, and list for less than $2.00 at summit.
As far as driveline, the front shaft between the two transmissions could conceivably be made quite short, something like a couple inches longer than just the slip yoke. As long as your careful with mounting, this shaft really doesn't have to do a whole lot of moving, as it will only change as your engine or the aux trans moves in their mountings. A limiting factor will be clearance for the shift rods and shifter, and clearance over the short shaft while maintaining a reasonable angle. My aux box is mounted with the input shaft about 3" lower than the output of the main trans if I remember correctly, this both gives the correct angles to the shaft, and provides clearance for the shift rods to transition to the side of the shaft as they connect to the shift lever. I forget the length of the shaft I have in front, but the front u-joint on the aux box is nearly at the back of my cab, so about 2 feet or so. Ed is correct in his concern about enough lengthwise room to squeeze it all in and keep everything in reasonable alignment.
The speedometer cable does connect to the output side of the aux box, as this allows the speedometer to be accurate no matter what gear combination your using. Since the speedometer gear in your aux box is likely to be setup for a different rear axle ratio, and speedometer gears for it are probably only slightly less rare than fresh dinosaur droppings, you'll need an alternative solution. Assuming your main transmission and speedometer combination are currently accurate: When you have the transmissions disconnected, carefully turn the output of each transmission while counting the revolutions of both the driveline and the speedometer gear. (you could also disassemble and count teeth, your looking to compare the ratio of driveshaft turns to speedometer cable turns). If they both turn the same amount, great you don't need to do anything but hook the speedometer cable to the aux box. If there is a difference, you'll have to get a ratio adapter to put into your speedometer cable to make the output of the aux transmission look like what comes from your main transmission.
Example:
Main trans. driveshaft turns 4 times per 1 revolution of speedometer cable.
Aux trans. driveshaft turns 3.5 times per 1 revolution of speedometer cable.
Your ratio adapter would need to be 4/3.5 = 1.143 to give you the same speedometer readings as before adding the aux trans with the cable attached to the aux trans.
I should probably find a frosty adult beverage and quit typing...
