Clearance is definitely a problem on my car.

When I took it off the jack stands clearance between the Manifow 3into 1 freeflow and the unit joint nyloc nuts is 1mm. I think it will hit on a bumpy road.

Ideas I have so far are:
1) double up on manifold gasket (it is that close) I wonder how long the gaskets would last, and if they'd give you any real movement...
2) try to adjust the angle of the engine slightly by loosening and refastening the engine mounts (no idea if that is feasible) won't change the position of the extractors in relation to the engine, so clearance will be the same
3) take to the extractors with a ball pene hammer (my last choice because the extractors are brand new) an exhaust shop may be able to put a bend in them for you

4) convert to different (pot?) joints unfortunately that's a pretty big job, the output shafts from the diff are different, so engine out. The driveshafts are different too