Short version: On OC_Peter's Speedster he had the 120A alternator and in order to make the 2.4 manifold fit he first shortened one of the bolts on the alternator by 1 cm, but the mani still did not fit (another 15mm was needed) so he had to modify the manifold too.
Some of the pictures show that it is the circular protruding part on the mani that still hits the alternator that is shortened. This protrudes the 15mm that is needed. I believe oc_peter sawed it off and then glued back the sawn-off part as a lid.
He also writes that the hole that gets made is not as large diameter as the part he sawed off. By sawing it off a hole quite a bit smaller in diameter gets created.
OC_peter modified both alternator bolt AND manifold, I'd guess you'll have to do both, otherwise one would have removed too much from the manifold.
And - yes - he is happy with the end result!
Haven't done this myself since I have the 100A alternator.