Peter,
You can remove the transaxle and bell housing with the engine in place. Ideally you will want to tilt the rear of the engine a little with a block and jack (but be careful not to crush the oil pan), so a) the rear transaxle mounts will clear the mounting tabs and b) the input shaft can slide backward,
It is also easier if you unbolt and can move the A/C condenser/shroud out of the way a little, no need to undo any of the A/C hoses or lose freon.
The clattering noise could be a number of things, but definitely warrants further investigation.
Julian
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