Here is an intake comparison between the 85.5/86 Mustang SVO upper intake and the 87-91 2.3L Mustang non-turbo upper intake.  When considering cutting your upper to rotate it ~90°,  you should consider the 87-91 intake.

intake top view
On the left is the 87-91 non-turbo intake and on the right is 86 SVO intake from the top.
The SVO upper (right) is not sand cast and would be hard to weld. Notice that the 87-91 is shorter across where the valve cover would be.

intake bottom view
On the left is the 87-91 non-turbo intake and on the right is 86 SVO intake from the bottom.
The 87-91 actually measures 3/4" shorter across the valve cover area. The square-bore holes are the same diameter on both intakes, so flow on the bottom side is not reduced. In addition, the bolt pattern is the same and will the match the SVO lower.
intake TB view
On the left is the 87-91 non-turbo intake and on the right is 86 SVO intake from the Throttle body side.
Also notice that the 87-91 intake is 3/4" shorter than the SVO intake.  This will be helpful when rotating the intake to allow for extra hood clearance. Both Throttle bodys measure 50mm ID.
4.6L vs 2.3L TB
On the left is the 96-97 4.6L Mustang Throttle body and on the right is 87-91 non-turbo intake from the Throttle body side.
4.6L TB vs 87-93 manifold ID
I think the shorter 87-91 intake will help get around the alternator when rotated 100-110° but you will still have to remove a slice from the intake.  The 4.6L Throttle body (TB) is very short but does require an adapter plate/modification to the intake in order for it to work.  The 4.6L TB measures 65mm while the stock is 50mm.  Unfortunately, the 4.6L unit does not have the Idle Air Bypass motor (IAB) so you will need to externally mount the IAB.  A better solution is to use a 94-95 5.0 throttle body.  I will have a detailed page on this modification soon!

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