Hi and welcome along,
I too have a Stradale, owned it a little over a week now, traded in my Brutale 800 for it. Not had much chance to open it up yet as I'm taking it easy until it's at least covered a couple hundred miles
How tall (short) are you? I'm 5'8" and I can touch the ground on toes with both feet, if I leave one foot on the peg I can stand flat foot on the floor with the other foot which is comfortable in traffic. I shall see how I get on with it as it is before I think about lowering it.
I certainly have to think a little more about stopping, like if I'm on a hill, get it into first then put left leg down so I can still hold rear brake etc, also leave the bike on its stand when getting on especially if the panniers are attached and then raise once your on board helps.
There are lowering links available for the rear shock to drop it a bit, my MV dealer said they have 3 options 20/30/40mm. There is also a 20mm lower seat available from MV. They also make a sports seat which appears to do away with the hump in the standard and lower seat options, that might be more comfortable, some switch to a Rivale seat to get rid of the hump but I've heard it's not as comfortable?
I've not had any of the numbness issues you've suffered, was out on it for 3/4hrs on the weekend and it was fine although the seat hump does limit your movement in the seat, good if a pillion is on board I suppose, I just had to stand up on the pegs for a few seconds just to stretch the muscles a bit and it was fine.
Looking forward to a few longer jaunts in the summer with the Mrs on the back and panniers full for some days/overnights away