What OS version did you upgrade to? If 4.6 or newer, see if you can boot up in safe mode.
See KB17877-How to start a BlackBerry smartphone in safe mode
I'm not sure what to advise at that point, assuming you are able to boot in safe mode. But at least you can experiment. I'm thinking maybe try a security wipe and delete all third-party apps, if you can even do that in safe mode.
Last resort, see What to do next if Jl Cmder will not connect and wipe - BlackBerryFAQ
and wipe the device and reinstall the OS. And http://blackberryfaq.com/index.php/I...Berry_Nuked%3F
may also be of help as far as the steps to connect to a blackberry that is not completing boot up.