[DSPTurtle]

My humble opinion is that you have moved the engine too far back. You should be able to use a normal engine mount in the rear and only mod the transmission mount. The down pipe will require a little "reshaping" with a hammer and/or vice. But, it all should fit and there is no way to modify the charge pipe unless you use silicone hose from the turbo outlet to the intercooler inlet.
By the way, are you using a K26 turbo or a K27? That will affect the fitment.