HD stopped using the tapered bearing for a while and went back to it in some models. It's stronger and more desirable. Lasts longer and takes a load better.
As for a counterbalanced engine: Generally, they don't take the abuse because the block is weaker due to now housing another shaft, and the counterbalancer is the weak point, as it's small bearings and shaft diameter become an issue at high RPMs and hard loads on the Harley engine.
It's not to say it can't be done, but it's one more thing to consider as it's a known failure point.
I think where most people see issues with on built up B motors is when they spin them up quickly at high RPMs then use engine breaking to slow it down. There's a local drag bike builder/dyno guy that takes B motors up to 7k regularly, and as of the last time I've heard, he hasn't seen a counterbalancer shell out. I agree tho, that it is another link in the chain that you have to think about.
Right now, I have my rev limiter set at 6200 rpms, I think most builders would agree that 6200 is a safe limit for the B motors. If I ever have to tear into the motor, I am still debating on whether I want to keep the counterbalancers or not and raise my rev limiter to 7k rpm. Until that time, I'll keep my eyes and ears open for ways to strengthen the counterbalancers so that will be a non-issue. I'm getting kinda used to how smooth the B motors run.
In regards to the crank bearings, there's conversions available to retrofit the '03+ A/B motors to the stronger Timken bearings. I'm still running stock bearings in my bike. But like I said above, if I ever need to get into the motor again and mod it for more horsepower/higher RPMs, I'll do the Timken conversion.
'Course if I had a Sporty project bike, I'd be building that up and not be concerned about crank bearings and counterbalancers. :lol8