All this has been awhile ago so I forgot another important detail. Lowering the engine causes the left motormount to pinch the shift-shaft which passes through it via a stock notch, immobilizing the car. With the small amount of down-and-back movement I did, I managed to lower the shift-shaft support under the left header just enough for clearance, and the shifter stick then aligned as-stock in the cockpit. The shifter rod is now quite close to the edge of the block, bellhousing and inner fender edge but everything clears. Good luck with more movement than this.
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