We've had customers complain about many of the manifolds on the market for the RB's not being able to fit the S30 chassis due to the vastly different engine bay real estate...
Here is the turbo placement we went with when designing one for a customer of ours (pictured is our S30 jig car):
The placement is very different then our other manifolds and can only expect the other manifolds made for the skyline and 240sx run into the same issues. However, the smaller turbo setups (usually found on the RB20's) fit on the straight forward manifolds and minimal clearance, but works.
Pictured is a Precision Billet 6766.
Hope you find success with your setup. Can't really speak for the issues you ran into but I've seen similar issues with all kind of setups come into the shop.