Sounds like it might be best to do the opposite of what I'm doing and lower the sub-frame a inch or so.
Longer bolts and spacers for the sub-frame mounts would work down below.
Same for the passenger side mount. They would have to go between the mount and the bracket that bolt to the engine.
The driver's side motor mount can be slotted on the body side to drop it down. You can even weld, or bolt, an extension to the top if you need to.
Front mount you would need slot the mounting points on the engine side, or possibly make a new bracket.
This would get you the clearance up top that you need for the intake and rear exhaust manifold. You'll lose some ground clearance doing it of course but as long as you don't try to slam it you should be ok. If possible I would see is you can raise the lower control arm mounts on the sub-frame side to keep the suspension geometry as close to stock as possible, otherwise if you lower the car it it'll be getting even further out of wack.