So I have a S2 Manual carb touring wagon its an 88 body. Captively nutted. I attempted a fix but was not quite as thorough as your job Bennie
So I buys a S1 85 touring wagon is great nic, had 126K. But its an auto, push button 4wd single range. Both cars were white.
So I does the manual conversion putting the 88 engine and gbox 5 spd dual range and the matching diff and drive shaft into the S1 85 shell. Seems to be going well, however the shifter linkages are about 2.5cm forward. I give up and cut the shifter well on the floor of the car, and extend the rear linkages rubber offset plate that holds the shifter assy to the under side of the tranny well.
All seems good, passes blue slip. But something is not right and its worse with the lift in. Lift is solid alloy blocks all round. Well everywhere they can be right. all the same 2 inch/50mm.
So I attempts to do small things to fix strange feeling.
Strange feeling is a looseness or pretty severe flex mostly when accelerating/decelerating. Going over bumps in neutral seems fine.
I had to jump start the car a few days in a row. Though for sure I was going to tear something apart. I think that the movement is at the gbox cross member. "Something" is causing it to move back and forward/up and down. Fingers under the 4x4 selector, from a standstill or low speed under full acceleration (webber EA82 300K + its not a powerhouse...) is almost painful with the pressure the lever pushes down on ur hand. when off load, it rides back to normal position. No lift to the back of shifter linkage assy, so I have used about 2cm of washers to space it down. Also had to drop a custom bolt in there, though not sure If im using it now or the original one. The back of the box seems to move a fair bit.
Now the stay bar from firewall to engine is tight and the welds seem good. Its a longer one from memory that was already in the 3" lifted 88 S2. Giving its a solid shake, everything seems tight.
Engine mounts also swapped along with the Gbox mounts.
Radius rods have Nolathane bushes. Though I feel this is an area that may be a issue. Not sure why I say that, just that its the general area where the issue seems to be.
Inner lower control arm bushes are new. Ball joints, tie end rods are all original to my knowledge (130K ish).
Hand on engine each side/head, give her a shake and the whole car shakes almost as much as the engine. Engine seems to be mounted to the car fine.
I have recently had the engine out to do the head gaskets. Same before and after engine out.
Car parked, hand brake on, push car back and forward in drive (flat concrete) and it feels like she is moving a bit too much, like something is not tight enough. Not hubs but back to front, Radius Rods again I cant but help thinking.
I have done a lot of tinkering with this car and the previous over the years but Im no mechanic, I read and take my time and work through things. But this has me stumped.
Im almost at the point of driving to the closest forum member who can help me nut this out.
Please help me guys, im lost!
That's just insane 
