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I had no issue with exhaust manifold clearance.  It isn't stock and it is close, but no issues.  I'll try to get some picts posted.  It will be late next week before I get time.
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on the 1st 16v swap we had no issues at all  but one of the swaps we did the manifold was really close to the frame where the flange was we used a 1/4" thick spacer  under the motor mt to get clearance  I would guess there are some differences in the stock manifolds which may have caused this  or a "flaw " in the frame

60 does seem pretty slow. I only have 30" tires but i hit 90 before i ran out of gearing. It will cruze all day at 75 though.