"i.e. it makes it a crime to perform an act that enables someone else to misuse a computer. Where 'Enable' is left so vague as to be meaningless. i.e. punish Peter because something he does enabled Paul to do something illegal."
Peter's modification to enable Paul's access would need to constitute an authorised modification in its own right. Otherwise, the loophole in the original Act remains that, if Peter, without authority, creates a privileged account on a system (for example), and then passes the details to Paul to carry out the exploit, Peter could not be charged under the Act.
In any case, s61, Serious Crime Act 2007, repeals s35(2) of the Police and Justice Act 2006, so this provision does not come into force.
"Section 3A makes it a crime to make cracking tools, networks sniffers etc. "
No, it does not. The drafting is not perfect, but, it is a criminal offence to create a tool "intending it to be used to commit, or assist in the commission of, a [computer misuse act] offence." If you write a packet sniffer for testing your network, the burden on proof would be on the prosecution to prove that you intended to use it to commit an offence. It has the element of "intention" - a mental state - and is not absolute.
It's not perfect by a long shot, but, it's not as bad as you point out, at least to my mind.
The drafting of s37(3), sadly, is entirely incomprehensible to me.