The following article provides information on retrofitting a Tremec TR-3650 5 speed manual transmission from a 2001 to present Mustang GT to a modular engine equipped **1992.5+ panther, demonstrated on a 2004 Crown Victoria.
Some of the information provided is specific to 2003+ vehicles, however this will still give you a nice overview of what is involved.

Note the powertrain management/pcm were changed drastically for 2005+ models which will add some complexity to the conversion, however you will not have any under-dash PCM clearance issues as with 2004 and older models (PCM was relocated to underhood/fender liner)
The steering column was also changed for 2005+.
Those who wish to retain power adjustable pedals (if equipped) will need to do more fabrication with the pedal cage.

Some additional related information for the manual conversion but instead using a T-45 transmission can be found here;
https://www.crownvic.net/drock96marquis/5speed.htm

**Early 1992 CV/GMQ/TC and all 1991 model Town Cars use a different transmission bellhousing pattern on the engine block (rather than the 'modular' style) to mate with the standard AOD transmission. This retrofit is not possible with the stock engine block with the above mentioned transmissions, but could be done with one using a matching bellhousing for 3.8/5.0/5.8l Mustangs (or other applications using the same engines) just as with the 'box' body 5.0/5.8 panthers.


The following was authored by 2004_p71 and was originally posted in This Thread
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Introduction

Few years ago i had the opportunity to drive and later own black&flames's 89 manual box.I still can remember the thrill of driving that car and how excited i was to drop the clutch for the first time.

Years has passed and i finaly got back that little thrill that i missed so much by doing the swap to my daily driver 04crown vic.
It sure bring it's part of challenge but it really worth each and every hour and money put in that project.

Finaly i would like to thank Jeremy (black&flames) for giving me such oportunities and all of you who have done this swap and have been very generous with your info and time quickcrownvic-quickvic30-Funkrider-Metroplex-drock96marquis

Thank you

This write-up is not an exact procedure on how to do it but should be used as a guide.I do not want to be held responsible for any misunderstood or mistake during the swap.
This swap should be done by an experienced mechanic with an appropriate facility.





Transmission

I have used a tremec tr-3650 transmission found in any 01/04 mustang.This transmission will handle better the hp/tq than the t-5 or t-45 found in older model but has it's own problem too.
The second gear syncro is prone to be difficult to engage when the temperature is cold outside.Ford has made an updated part to resolve that problem and most 04 tremec should not have that problem.That transmission is rated at 360lb/tq and should be fine in most application but if you need something above that i would recommended an up-dated version who can support up to 495lb/tq (see my links at the end)




Clutch/ flywheel


For the clutch/pressure plate i went with center force.It is a 10 spline unit who was made for the mustang cobra.It require a bit more effort to depress the clutch but it really hold the power.
The unit is quite pricey but you cant really so shop wisely.



The flywheel is a 6 holes billet steel 1:1 ASI approved.
I have been recommended to NOT use a billet aluminum for this application.




Clutch pedal assembly.

I went with the 01/04 mustang brake clutch pedal assembly as a starting point.The mustang cable clutch assembly cannot be used on the crown vic as is so it had to be modified to fit my existing brake pedal.






You will need to grind off the clutch pedal shaft off the mustang assembly to later weld it to the crown vic assembly.
Pay attention to the clearance with the pcm when you will weld the shaft. Mine has about 1/4 inches in between.








The clutch pedal itself has to be modified.
You have to drill a hole approximately one inch lower that the original position and make it square with a file.
Do not mess up with that step as is the square hole is too large the pedal will spin on the shaft.




This will make the pedal still sit lower that the two other pedal but since the fuse box is right up there you dont really have the choice. It may look weird but the feeling when you press the clutch isn't.




Since i welded the clutch shaft there is no more space for the brake light switch who was original mounted below the abs switch so you will have to mount your own on/off switch directly below the shaft or at any other convenient place.

The electric harness for the automatic is obviously no longer needed. The only wire who should remain from this harness are the one for the oxygen and vss sensors.You will have to run 2 extra wire for the reverse light.

A pcm reprogramming (aka a tune)is mandatory for this swap.
I highly recommended lonnie at blue oval chip. he is specialized in unique swap. (see links at the end)



Crossmember


The crossmember on any 03+ model has to be modified in order to clear the taill of the transmission.The top has to be cut as well as the front of it.
Even the lip at the bottom end of the transmission needs to be remove
This step is quite time consuming since you will have to make sure there is absolutely no contact in between the two parts.
A gap of 1/4 between the crossmember and transmission is required since everything will move during driving condition.







Drive shaft

You need to change the 36 spline yoke for a 28 sline yoke.

A 5/8 length drive shaft spacer must be used since the new transmission is shorter than the 4r70w/4r75w.
Most aftermarket companies makes them for the mustang but be aware that they used smaller pinion flange so it will not fit the panther's.
It's either you get one custom made at the local machine shop or you swap the pinion flange and joint for the mustang one.


Shifter


A rectangle of 3 by 5 inches has to be cut approximately 3 inches from the abs module for the shifter location.
You will also have to trim a bit of the reinforcement underneath the tunnel at the bottom of the rectangle to again clear the transmission.

I have used a hurst short throw shifter.The base is for obviously the tremec but the shifter itself is for the older style of mustang (the fox years).
It is close from the dash but there is plenty of space for your hand.






parts list


Tremec tr-3650 01/04 mustang
center force clutch/pressure plate
Flywheel 6 bolts
Flywheel bolts F6ZZ6379AA
clutch lever XR3Z7515AA
clutch cable XR3Z7535CA
Clutch bearing F7ZZ7548AA
pilot bearing F6ZZ7600A
Dust shield F6ZZ7513AA
Yoke 28 spline E9TZ4841A



I will up-date this write with your comments and help in order to make it as complete as possible.

If you need more info or have any question i will be glad to answer them all.
you can pm me or write me at p71c1@yahoo.ca

Good luck with this swap.

heres some video of the final results enjoy

http://www.youtube.com/watch?v=2PgNDNamCMY
http://www.youtube.com/watch?v=GXUqY8iAzhs
http://www.youtube.com/watch?v=9MKg-jcTZS4


And a picture of the completed swap;



-----------Courtesy 2004_p71