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The 6 speed is not going to be hard to find for MSRP or under. Dealerships trying to sell it for over sticker are stupid. The 6 speed on the Accord is very similiar to the CL's, but not exact. As Samson said, the entire CL line is selling poorly...a CL-S 6 speed can be had for close to invoice.

Your two theories on the limited production are both correct.