If the top one has gone normally something else is amiss, check you've got the right heads on the right barrels, i.e. not an R barrel and an SP head on the top. Also while it's apart, have a look what jets it's running, in theory it should be a size (or maybe two with the head conversion) leaner on the top.
Put your finger over the plug hole and push the kickstart, you should feel pressure, a fiver (and the feel of the kickstart when I was there) says there'll be nothing there.
Have fun, chopping the top is a pain, tank off at the roadside unless you live at the top of a rise just after a 120mph straight
Re. will the barrel live without a replate? Maybe, it'll certainly have some level of damage and no pro engine builder is going to recommend running a damaged barrel at all, but there are several out there running fine that I know of with pitting and/or a cracked bridge.
You wouldn't think mine would last if you looked at it, there's some pitting on the bridge that you can feel. I was dubious but Steve said it'd be OK and it has been.
It depends how you view it and what you want, if you want it as reliable as possible and don't give two hoots how much you know about what's what then have a reputable builder fit a new Honda barrel (or replate yours) and piston kit, follow their running in guide and get it back to them to check the jetting. But as you've found having someone else do it is no guarantee it won't go pop when used in anger, there is no substitute for real world testing. It's also going to cost somewhere the wrong side of £300.
Or rip it down and see how it looks, you never know, you might get away with a bit of wet and dry on the barrel and a new piston and rings.
And that's my point, knowledge of what will or won't work comes from finding out, sometimes the hard way.
Or talk to Andy, he loves taking them to bits, he wanted to swap my barrel the other weekend for no good reason
This in no way condones the use of less than perfect parts, do so at your own risk
or when you realise the piece of outdated junk will die anyway, no point burning a £50 note when you can burn a fiver and get the same result!
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Please do not PM me technical questions, if you can't find it on the Forum start a thread