Have a similar problem with my bike which I put down to a combination of crappy ergonomics, poorly designed seat and the forward controls on the cruiser. And being a shortarse whose legs are stretched somewhat to reach said forward controls (which I think has more to do with the problem than anything else).
Initially I thought it was a case of breaking in - both of my arse and the seat, seeing as I hadn't ridden for a few years. Soreness and numbness started to set in after as little as 45 mins in the saddle, and became pretty bad, almost unbearable, after I'd gone 300k's or so. 
Having clocked up 9000km in 4 months, I thought my butt would have HTFU'ed. I'm getting a custom seat (eventually), but in the meantime I bought a sheepskin off Tardme for $20, doubled it over and bungied it to the seat. Testing ground was Auckland to Wellington in one go. Other than standard pit stops for gas and lunch, managed it in one go, and was no more sore than if I'd taken the cage. Blardy magic ! 
On the return trip I was getting a bit sore by about the 2/3 stage, but just had a 30 minute coffee stop and rode the remainder.
Catapultam habeo. Nisi pecuniam omnem mihi dabis, ad caput tuum saxum immane mittam!
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