CR500 early vs. late pipe compatibility?

Had the idea of a no-radiator CR500 AF swap, but the air cooled CR5s had a high-routed pipe, which will be a problem with a perimeter frame and modern shock. Will the later pipes that go low under the shock reservoir on a modern bike work well with the porting of the air cooled motors?

They used the high routed pipe through 88 on the 500 and people still use the lower style pipes on the older engines in their AF conversions. But, I don't know if there are any differences at the connection to the engine for air cooled and liquid cooled.

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