As far as I remember you can't do it all from underneath unless you are an experienced proctologist. The air cleaner assembly is above the manifold and removing that means removing all the duct work on the firewall etc. The guys at Autologic did mine as well as the PCV valve and the glow plugs at the 200K service.

I would be very interested to see your comaprison between the manifolds. Check to see if the ports match the gasket. The one I saw on the net had the EGR port coming off cylinder one only. Having less exhaust gas in the intake tract is not ideal for emissions, but I am not sure what effect there is on partial throttle tune. Closed or Full throttle will be unaffected.

Cheers