So, if the top tube is shorter, you should be rotating your pelvis back. That is, more upright, onto your ischial bones. Ok, now, what exactly hurts?

1) Do you get the sensation of being 'forced apart?' In other words, is the pain somewhere on the inside of the sitbones? Saddle too narrow or set too far back.
2) Is it direct down pressure pain on the ischials? Possible road shock transmission that you didn't feel before you rotated the pelvis onto those bones. An inch shorter tube up top can make a difference.
3) Is it pressure on the perineal/pubic area? Usually associated with riding the peak by tilting the saddle too far down in front. You work your way onto the peak.

I also have geometry difs on my two main bikes. That's why, after failed attempts, I went with Brooks. I'm not saying you should. It just worked for me. The leather is not backed by anything except a skeletal frame. They have formed to me and the geometry both. Thus, although the model is the same on both machines, they are now actually a little different, I suppose.

It may not be possible to use a single saddle of the type you have. Don't they have a backing platform of some kind? If so, I'm not certain they will ever re-form to a different sit.

Oh yeah, one more Q? Are you a Clydesdale, like me, at 225 lbs with heavy bone structure(read: full stern members)? If so, and you have shortened your cockpit length, you may have to go with a wider saddle on the shorter bike.