I was in the same boat last month. Was trying to fit up a J od with a D driveshaft.
Unfortunately I reached the same conclusion as you.

However I was not big on choice #1. There did not appear to be enough clearance between the bolts and the shoulder of the flange.

I sort of like choice #2, but that looks like a lot of machine shop work and for the cost, it would probably be just as worth it to me to just have a large flange M40 driveshaft shortened.

Fortunately, with a 140 I have no issue fitting a large driveshaft through the tunnel.

Others have spoken of a small flange for a J, but I haven't come across one yet. If you do, let us know.

In the end, I ended up using a D-type od behind my B20 on the '70 145. Basically because I already had a driveshaft that fit. Would have prefered a J-type though since that speedo gear was set up for the 4.10 rear end.

In your case I'd go option 3, 2, 1.
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Tom - '60 544, '68 220S, '70 145S, '86 745T, '06 Mazda MPV