Dimensions
I took some dimensions yesterday just to make sure everything appears like it's going to line up. So these dimensions are kind of just an FYI for others in the future.
Distance between trans/engine mating face to the first bolt hole center line of trans mount ~ 21.5 inches.
Note: both the 5spd & 6spd were the same, (hence being able to use the same trans subframe).
Overall 6spd length from trans/engine mating face to the end of the rear drive output surround - 34.5 inches.
Overall 5spd length from trans/engine mating face to the end of the rear drive output surround - 32 inches.
Length of the 5mt front driveline from the end of the input shaft to the center driveline flange – 29.5 inches

Length of the auto front driveline from the end of the input shaft to the center driveline flange – 27 inches

Length of the 5mt rear driveline from flange to flange – 33.5 inches

Length of the newer style auto rear driveline from flange to flange – 31 inches

In the comment above and in my pictures I reference the "newer style" auto driveline. This is due to the fact the new rear diffs are a little longer than the ones found in the first gen Legacy, and as such the rear driveline lengths are shorter.
Note: I've updated the numbers above based on my measurements of the transmissions and drivelines outside of the car. Everything looks good and the length differences work out perfect.
Parts
This is a list of various parts I have picked up for the 6spd conversion and some notes regarding them.
Driveline – As noted above, I’m intending to use the front section from the automatic Legacy driveline with the rear section from MT Legacy driveline.
Transmission subframe – Again, as noted above the transmission subframe is the same between the 5spd & 6spd.
Rear diff & axles – I’m keeping all the stock Legacy rear end.
Lower flywheel cover plate - The plates are different between the 5spd & 6spd, so you'll need to get the 6spd. I'll take some pictures comparing the two, but here's a thread on NASIOC with more info.
Lower flywheel cover plate - Qty. (1) - 30216AA040
Pic of both below (5spd top & 6spd bottom). Note the larger bulge/area for the presssure plate to clear.

Clutch & pressure plate – I’ll be running the 6spd clutch & pressure plate. I decided to stick with the stock Subaru flywheel, clutch, & pressure plate. Driving with a LW flywheel in traffic isn't fun. Additionally, I decided to go with the stock Subaru clutch because of complaints of decel rattles with the non-Subaru Exedy unit. More info can be found in this thread on NASIOC.
Here's a note and picture regarding the alignment of the flywheel & pressure plate. The dots on them should be aligned 120 deg. or more apart from each other. Those spots are areas of residual unbalance.


Throw out bearing, clutch release lever, & clutch slave cylinder – The throw out bearing is the same between the turbo Legacy/WRX & 6spd. The clutch release lever is different and the 6spd lever must be used. I'm going to try and keep the turbo Legacy clutch slave cylinder.
Here is a picture of the 6spd (left) and 5spd (right) clutch release lever for comparison.

Starter – the 6spd starters are slightly different in depth than the 5spd starters, so you’ll need to pick up a 6spd starter as well.
Front axles – you can run the Legacy front axles by getting axle stubs that were on the early 2004 MY 6spd’s. I’ve listed the seals as well in case you want to replace them as well. To replace the seals, you'll need to remove the bearing caps. More info can be found in this thread.
6spd axle stubs - Qty. (2) - 38415AA110
Axle stub circlips - Qty. (2) - 805329010
LH axle seal - Qty. (1) - 806730042
RH axle seal - Qty. (1) - 806730041
Drain plug gaskets – below are the two drain plug gasket part numbers. If you have a 6spd with a sump, there will be another drain plug and gasket.
6spd drain plug gasket - Qty. 1 - 803926070
6spd oil sump drain plug gasket - Qty. 1 - 803916080
Trans mount – The 5spd & 6spd trans mounts are different. The 6spd is a little bit shorter in height. If you want the hardened mount, most of what everyone will be selling is the SPT trans mount. Its part # is D1010FE000. It is not the STi trans mount, its part # will start with ST, but from the research I’ve done, they should be the same hardness. This mount is a little different than the 5spd mount. It is not covered with a shiny black coating. It’s more a dull rubber, like the stock mount. Also, the exterior of the mount appears to have a “softer” durometer rubber and the inside is supposed to be stiffer. It’s a little hard to prove all this, but I feel confident in the research I’ve done and people I’ve talked to.
Speed sensor – If you are swapping this into a US first gen Legacy then you’ll likely just unscrew the electrical sensor and install the mechanical one to hook up to the cable. However, if you’re installing the 6spd into another Subaru model with electronic speedometer, you’ll need the plug for the stock sensor (or you could swap your stock trans speed sensor). There appears to be an extension harness you can buy that goes between the speed sensor and chassis harness. The part # for this harness is 81881FA010. This thread on NASIOC has more info. Here are pics of the stock 3-pin speed sensor.
Reverse & neutral switch electrical – The 6spd reverse & neutral switch connectors coming out of the transmission have the same connectors as the 5spd, but are shorter than the 6spd harness. So I depinned the 6spd connector, did the same thing to the 5spd connector and repinned the 6spd wires to the 4-pin 5spd connector.
Center diff electrical – I depinned the wires from the stock 6spd connector and used a clutch master cylinder low level connector and a chassis side ABS wheel sensor connector (you could use an ABS wheel sensor and chassis side harness if you have one) and repinned those two wires. I will be making a plug & play harness to the existing AT plugs to bring the wiring in the cabin.
Here are two pictures of the final connector/plug setup.


DCCD controller – I’m planning to run the aftermarket DCCD controller from DCCDPro.com. When ordering the controller, make sure to let them know that your TPS voltage is reversed, assuming you are still running the older style throttle positioning sensors.
As a note for installation of the DCCD controller, I found that there was not a great location behind the dash for the controller. In addition, if you install the controller behind the dash the standard length of wires will not be long enough for the G sensor to reach the required installation spot near the e-brake handle. I decided to install the controller under the center console where the automatic seat belt brackets were located. Since I converted to the manual seat belts, these were not be used. I had to modify the brackets to get the controller fit. More details and pictures can be found in my build thread. Another possible location could be under the passenger seat carpet where the ABS computer is normally located. If you don't have the ABS computer, this could be a good spot. If you do have the ABS computer, you still may be able to squeeze it in there.
If you choose to install the controller behind the dash, make sure to request some additional length be added to the G sensor wiring, and the control knob wiring (if you plan to install them in the blank next to the e-brake handle.
Modifications
Starter – Since the newer motors have an 8-bolt setup vs. the older 4-bolt setup, you'll need to do something for the lower starter mount hole. The best option is to use an M14x1.5 bolt aprox 40-45 mm long. You'll need to tap the lower bolt hole on the trans and drill out the lower bolt hole on the starter to 9/16". More info can be found in this thread.
Pressure plate – There are three more bolts holding on the 6spd pressure plate, so you'll need to get these as well.
Exhaust hanger - I'm assuming some modification will need to be done, but I'm not sure what will be needed at this time.
Rubber shifter mount - The 6spd mount only has four mounting holes vs. the original Legacy six mounting holes. You will need to mark and cut or punch the extra holes. I used a paper hole punch. It mostly worked. I ended up bending the hole punch so don't use your wife/gf's good hole punch for this.
Here's a picture of the mount with the punched hole.

I’ll update the thread as I get to the swap and if others have additional comments to add.