Cloning is not the way to go, due to the configuration of Exchange being stored within active directory. Luckily, meticulous documentation is probably not required.
I know it may not be the answer you're after, but seeing as you're only adding a second CAS+HUB, simply installing server (2008 R2 I assume?) takes about 30 mins, put the SP on (another 30 mins?) and all the WUs (a good while, but its easy!) and installing Exchange (not too long, < 1 hour) may be the most time efficient way to do it.
The CAS and HUB roles will pick up the policies from the domain. The only real things you've got to do is setup your IP addresses and virtual directories.
However, as you're adding a second CAS, I am going to assume some form of NLB which is the biggest thing to do here as this may affect both the new, and the old CAS. Not something SCCM could have solved anyway - always a manual approach and planning required.
So in summary, do it manually.. it's not actually as bad as you think it is, because most of the config is stored in AD and it'll pick it up.