Transmission alignment.

I'm referring to the orientation of the transmission in relation to the tunnel not the engine. Here's the problem, I recently replaced my clutch (and bearings, etc) and upon reinstalling the whole shebang I find myself faced with an entirely new issue, I'm now attempting to reinstall my shifter but the transmission is now cocked slightly to the right (drivers side). Any clues as to the cause would be greatly appreciated.
 
That's the only variable that's changed, the old transmission mount was torn in half so I replaced it while I was down there. Seeing as it's a brand new OEM mount I can't help but doubt that the mount is the problem though if lined up just fine before the addition of the new mount. And before it's brought up no I don't have any gaps between my transmission and my engine either, I've double checked that as well. This has had me scratching my head for days now.:bang:
 
Re this misalignment: Is it that the rear of the transmission is now pointing more toward the driver's side rear wheel (i.e. engine/trans has rotated about Z-axis) or is it more like the engine and trans has rotated clockwise (viewed from the front) so the shifter now sort of points toward "11-o'clock" instead of "12-o'clock"?

If it's the former: If you unbolt the trans mount, does the engine and trans attempt to "relax" back to center? Do you still have the old mount and can you place it in there temporarily to see if the relationship is better?

How are the engine mounts? Any chance one has given up and collapsed, allowing the engine to drop on one side (e.g. the driver's side mount?)

Has the car ever been in a collision?

Has the K-member ever been out of it?

I know you said you checked but I'm going to ask again anyway: Are you absolutely sure the transmission bellhousing is fully and completely seated against the block? That the trans input shaft went into the pilot bearing properly, that no dowels or anything else is cocking the assembly?
 
Re this misalignment: Is it that the rear of the transmission is now pointing more toward the driver's side rear wheel (i.e. engine/trans has rotated about Z-axis) or is it more like the engine and trans has rotated clockwise (viewed from the front) so the shifter now sort of points toward "11-o'clock" instead of "12-o'clock"?

If it's the former: If you unbolt the trans mount, does the engine and trans attempt to "relax" back to center? Do you still have the old mount and can you place it in there temporarily to see if the relationship is better?

How are the engine mounts? Any chance one has given up and collapsed, allowing the engine to drop on one side (e.g. the driver's side mount?)

Has the car ever been in a collision?

Has the K-member ever been out of it?

I know you said you checked but I'm going to ask again anyway: Are you absolutely sure the transmission bellhousing is fully and completely seated against the block? That the trans input shaft went into the pilot bearing properly, that no dowels or anything else is cocking the assembly?

The first description is dead on, unfortunately no I didn't support the engine when the transmission was out, though only because I couldn't. There's a skid plate like piece that sits directly under the oil pan (I'm assuming it's an aftermarket piece added by the previous owner after lowering the car) which the oil pan already basically rested on.
 
Also no the k-member has never been out of the car, at least not during my ownership and yes I'm certain there is no gap, I've inspected it from top and bottom, when the transmission was installed aside from needing to wiggle the engine a little everything lined up and slid together like it was on greased rails.
 
I've never actually done it so this is a "throwing it out there" question: Is it possible to install the transmission crossmember "backwards"? If so, perhaps it has a bit of an offset built into it and you're seeing that.

Maybe you can support the back of the trans, remove the cross member and see if flipping it 180-degrees will allow things to fit better.

Again, just throwing it out there...
 
I've never actually done it so this is a "throwing it out there" question: Is it possible to install the transmission crossmember "backwards"? If so, perhaps it has a bit of an offset built into it and you're seeing that.

Maybe you can support the back of the trans, remove the cross member and see if flipping it 180-degrees will allow things to fit better.

Again, just throwing it out there...

Actually that is an interesting question, oddly enough the crossmember is stamped with marking denoting which side is the top side and which side is left and right...I think top and bottom are obvious enough not to need a stamp but I'm curious as to why left and right matter, there might very well be an offset left to right, in my case though this is a non-issue obviously seeing as I noticed these markings, secondly I pulled the crossmember last night and the tranny is resting on a jackstand and it's still out of whack.:scratch:
 
I probably wont be of much help, but since trans mount was replaced, it may be that the motor mounts are torn too. While putting a trans where it should mount on a brand new car, this has caused the trans to be misaligned with the motor, not the other way around.

So to be not as confusing, and since you have the car apart, why not replace the motor mounts too (if they haven't been replaced recently)?
 
I probably wont be of much help, but since trans mount was replaced, it may be that the motor mounts are torn too. While putting a trans where it should mount on a brand new car, this has caused the trans to be misaligned with the motor, not the other way around.

So to be not as confusing, and since you have the car apart, why not replace the motor mounts too (if they haven't been replaced recently)?

I get what you're saying, I don't know if that's possible but it's something I'll look into when I crawl back under her tomorrow. I would like to replace the motor mounts seeing as they're old and worn but I'm trying to repair her on a budget right now, if I can't find anything else I may resort to that though.
 
Pile on here. +1 on the motor mounts. Usually the motor mounts break and that causes the transmission mount to break from additional stress.

For a 97, the mounts are 13 years old. Typically manual transmission cars are tougher on motor mounts than automatics. For an older car, that further adds to the possibility of a broken motor mount.

Double if the motor was allowed to "hang" from the mounts during the transmission install. :nono:

IMO, the misalignment is from the motor being lower in the K-member on one side than the other. The natural twisting torque of the motor is going to tend to do this.

One method to support the motor is with an inexpensive screw type jack. A spare tire x-style jack will work as well. And finnally, there the "jam a scrap piece of pipe/wood in the K-member method".
 
Quick update for all the helpful gentlemen that came in with advice, I crawled under her last week and found that my motor mounts (both) were pretty much nonexistent, so seeing as the mounts were shot and the tranny had been pounded on a bit before I got her I took her to a local shop (with a good reputation obviously) and had them rebuild the tranny and install new motor mounts. I would've rather handled the work myself but work has been busy this week and I need her back on the road asap so $1600 later I'll be picking her up Monday before my shift.