I went from an E cover TE-60R, which fit perfectly, to an S cover equipped 6776 journal bearing turbo which had the discharge of the compressor cover pushed all the way over, so that the discharge lined up with the inlet of the intercooler inlet on the drivers side, but had a step on the passengers side of the hose. I did try the fitment on my current H cover equipped 6776RHPS turbo and the alignment was terrible. I agree with 87NAT, you will have to modify the intercooler neck and possibly the brackets depending on what headers and downpipe you have, in order to get any form of decent alignment. In the beginning, the PTE Stock location intercooler was never designed to work with an H cover equipped turbo. It was mocked up on a stock '87 GN that had a GT3255E turbo on it. It is only rated to support 750 flywheel hp, and the PT67 turbo can support 780 fwhp with an S cover. However, some have pushed the intercooler harder.
I really liked my PTE Stock Location IC, but I did not want to cut it, or have to deal with making or modifying the bracket. Hence the change with my combo. To my knowledge, 87NAT is probably the only member that has worked out the issues with installing this intercooler with an H cover equipped turbo. I bet all the negativists would think differently if they were to see pictures of your modifications. Pictures have a way of really clearing up the details. I wish I would have had my camera in hand when I was mocking up my turbo, during my IC swap.
HTH
Patrick