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Hi James here. Here is some information on the transaxle external controls.
The manual shift mechanism is made up of the following components:
The gearshift lever is connected to the transmission control selector housing and allows the driver to select a gear.
The transmission control selector housing transfers the gearshift lever movements to the transmission gearshift rod and clevis. The transmission gearshift rod and clevis is connected to the shift lever shaft (7C355).
A gearshift stabilizer bar is mounted to the transmission control selector housing and rubber mounted to a bracket at the RH transaxle support insulator.
The stabilizer rod equalizes powertrain movement with the transmission control selector housing and prevents the transaxle from being pulled out of gear by powertrain movement.
Rubber boots are provided for protection of the shafts and for sound insulation. Adjustment of the external linkage is not necessary.
Raise vehicle on hoist. Refer to Section 00-02.
Loosen shift linkage clamp bolt and place transaxle in neutral.
Unsnap boot bezel from console and slide gearshift lever boot up gearshift lever.
Disconnect shift lever housing insulator from retainer and slide up gear shift lever.
Install Gear Lever Aligning Tool T94P-7025-FH onto gear shift lever and rotate top of tool clockwise.
Locate access hole in center of underbody heat shield. Install MTX Shifter Alignment Tool T96P-7B140-A through access hole and into shift lever housing.
Screw MTX Shifter Alignment Pin T96P-7B140-A into shift lever housing until hex portion of tool bottoms lightly on shift lever housing.
Tighten shift linkage clamp bolt to 16 Nm (141 lb-in).
Remove MTX Shifter Alignment Pin T96P-7B140-A.
Turn upper portion of Gear Aligning Tool T94P-7025-FH counterclockwise and remove tool.
Install shift lever housing insulator on housing retainer.
Install gearshift lever boot bezel into console.
It seems there are special tools for aligning the mechanism, but you may be able to correct your concern without them.