Technical Notes
The following is some of the more obscure information I picked up along this project, and should definitely help out anyone looking to do a similar conversion. There is a decent amount of information regarding how to deal with the electrical issues that arose from an AT to MT swap. Due to that, the electrical section will have it's own page.
Return to Swap Intro
General
Fuel System
Suspension
Drivetrain
Electrical
The main issue I can see being asked over and over again is, "Will everything bolt up?" Yes, all the bolt holes are there in the chassis. All you need to do is remove the little plastic covers. I know it's cliché to say, but for the most part everything was "plug and play". The only exception to that was for the clutch master cylinder. I go into more detail on that in the drivetrain section.
Fuel System NotesThe fuel system is pretty straight forward and obvious on what needs to be swapped.   Swap gas tanks so the driveline 
will fit.   The only exception to that was the fuel separator, which is part of the evaporative emissions control system.   
This little device is only found on AWD equipped cars.   Why?   I don't really know.   It's nothing more then a sealed 
plastic container.   It has two lines at the bottom and one at the top.   On the AWD gas tanks there are two vent lines.   
They attach to the two bottom lines of the fuel separator.   The line at the top of the separator goes to the charcoal 
canister, which then leads to the canister purge solenoid.
An alternative to using the fuel separator would be to use a brass T or three-way manifold.   You'd hook up the two vent lines
and the line going to the charcoal canister to the manifold.   I don't see an issues to doing this instead.   You'll just want
to make sure you mount the manifold at a higher elevation then the top of the gas tank, or at about the same level that the 
fuel separator sits.   This will minimize the chance of fuel traveling into the evaporative emissions system.
Here are a few pictures of fuel separator
Sedan
    
    
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Wagon
    
    
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There were two main issues I ran into with the suspension.   The first was ride height.   I was a little unsure what my ride 
height would be like after the swap.   The main reason was that the AWD rear struts are different then the FWD rear struts.   
The mounting point on the hub for the AWD struts is raised slightly compared to the FWD rear hub.   Also it's moved forward 
slightly from the centerline of the hub.   The FWD rear mounting point is at the centerline of the hub.   So with that 
change alone, I was not quite sure how it was going to sit.
The second issue about the ride height was the struts.   I wanted to use KYB's AGX adjustable strut instead of their GR2 strut,
which is non-adjustable.   The only problem with this was KYB didn't make the AGX's for the 1990-1991 Legacy.   They did 
however make them for the 1992-1994 Legacy.   I called KYB and talked with one of their engineers.   He was nice enough to 
look on the drawings and tell me the difference between the 1990-1991 and the 1992-1994 AWD struts.   This is what he found 
out.
The spring perch on the 1992-1994 front AWD strut is 1/2" higher, compared to the 1990-1991 front AWD strut.   The 
damping was also slightly firmer on the 1992-1994 front AWD struts, compared to the 1990-1991 front AWD strut.
The spring perch on the 1992-1994 rear AWD strut is 3/4" lower, compared to the 1990-1991 rear AWD strut.
So with changing struts in the rear and the differences between the model years, I really wasn't sure how the ride height 
was going to turn out.   After I was all done, I took measurements to compare them with what I had taken before.   I was 
surprised.   They really didn't change much.   I gained 1/4" of ride height from the whole swap.
Here are my before and after ride height measurements.   They were taken from the ground to the bottom of the body sill, 
at the jack mount points.
Before Swap
| Left Front: 7" | Right Front: 7" | 
| Left Rear: 6.75" | Right Rear: 7" | 
| Left Front: 7.25" | Right Front: 7.25" | 
| Left Rear: 7" | Right Rear: 7.25" | 
I ran into one minor issue, and two main issues with the drivetrain.   The minor issue was with the STi short throw 
shifter.   I wanted a short throw shifter, but the shift linkage and mechanism had changed slightly over the years.   
The STi short throw is a complete unit, which was nice because it replaced all the old components with new pieces.   
All I had to do so I could use the STi short throw shifter was switch out the older style linkage piece on the 
transmission's shifter rod with the new one.   The only other complication was the bolt that connected the shifter arm 
to the linkage piece.   For some reason the factory uses a bolt that has a wider diameter body when compared to the 
bolt's threads.   I drilled out the top portion of the shifter bracket so that it was the same diameter hole as the 
bottom.   I then went to the hardware store and picked up a bolt that fit in the bushing.
Here are some pictures of the linkage piece and the bolt.
    
    
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The first main issue I had was with the rear differential member or mount.   I had ordered an STi differential mount 
for a 2002+ WRX.   It turns out that the mount is different.   The WRX mount is wider and the mount points are 
horizontal with the mount.   The rear differential mount for the 1990-1994 Legacies is smaller in width, and the 
mount itself is mounted in the rear crossmember at an angle.   I talked with 
Rallispec about the issue.   There are apparently three 
different types of rear differential bushings.   For the 1990-1994 Legacies & 1993-1994 Imprezas Subaru used a 
bracket that mounted to the differential and crossmember.   From 1995-2001 the bushings were in the crossmember 
itself.   In 2002 Subaru went back to the bracket, however as mentioned above, it's a different size and shape then 
the old bracket.
The second issue was with the clutch master cylinder.   The transmission I put in my car utilizes a hydraulic 
clutch.   In 1990 the only style clutch available in the Legacy was a cable operated clutch.   Subaru did not 
introduce a hydraulic clutch to the US market until the 1991 model year.   The hydraulic clutch was only 
found however in the turbo Legacy.   The normally aspirated Legacy still had the cable clutch.   Since there 
was an option/need for the hydraulic clutch, the factory started cutting out the holes in the firewall for 
the clutch master cylinder.   Those chassis that were to be turbo Legacies utilized the hole.   Those chassis 
that were to be normally aspirated Legacies had a rubber plug inserted into the hole.
What did all this mean for me?   Well I had to make a template from the pedal assembly so I knew where to cut 
the holes in the firewall.   It's not the easiest thing to drill/install the clutch/brake assembly on any car, 
especially one that it was not designed for.   Another thing I did notice was that the mounting bracket for the 
clutch pedal assembly was shorter on the 1990 model year.   So one of the points where the pedal assembly mounts 
to the car has nothing there.   I've looked at it, and feel it's not a real big issue.   I can see a very slight 
flexing in the pedal assembly, but both the brake and clutch feel fine.
The clutch master cylinder issue I had should not be a problem for anyone attempting an AT to MT conversion on 
a 1991 model year or later Legacy.   However for those few with a 1990 Legacy that want to attempt this project, 
I'm going to give you a large helping hand.   I've transferred the template I used to cut out the master cylinder 
holes into Autocad.   I had some issues with scanning the paper template in and printing it out to retain the correct 
dimensions.   I will provide the template in the original Autocad file, a PDF file, and a JPEG image.   When printing 
any version of the template out, you need to make sure you disable any scaling, and that it prints 100% of the original size.   
I've added a 4.5" line on the template.   If that line does not measure 4.5" exactly, the template will not have the 
correct dimensions.   From what I have found, the JPEG image does print with the correct scale as long as you don't 
use a Microsoft imaging product.   Go figure.   I'd suggest transferring the template to a piece of cardboard 
since it's more sturdy.
Clutch master cylinder template
Autocad 2000
Adobe PDF
JPEG Image