Hi. I missed part of your question on the Clifford aligning with the original (I assume you mean the original exhaust).
The Clifford's with the lower water chamber it is just too large
vertically for the original exhaust to fit. The water chamber adds about 1"or so in height thickenss to the intake on the lower side. According to Clifford the cast iron Fenton headers will not clear it without some severe machining & modifying.
This is why I followed Clifford's reomendation & went with the shorty tube headers to eliminate any machining which likely would not look too good & would end up with some thin walls to the cast manifolds.
I will have mine all assembled & installed next week & then I will know how it all fits & works.
Jimmie