I sorted this by installing pear again. After downloading go-pear.phar then running
sudo php -d detect_unicode=0 go-pear.phar
In the install there are options to change directories pear is using. They were already set to the correct locations for my new php such as /usr/local/php5/bin
I then had to add that path to my bash_profile for the pear command to be recognised.
export PATH=$PATH:/usr/local/php5/bin
To get pecl working again I removed pecl from /usr/bin then symlinked to the pecl in /usr/local/php5/bin
sudo ln -s /usr/local/php5/bin/pecl /usr/bin/pecl
The first package I tried to install was APC and I got the error
Cannot find autoconf. Please check your autoconf installation and the
$PHP_AUTOCONF environment variable. Then, rerun this script.
ERROR: `phpize' failed
This was sorted by following instructions from phpize won't work on Mac OS X Lion I used the homebrew solution
UPDATE: I installed PHPUnit fine then ran phpunit --version
This gave an error of
PHP Warning: require(/usr/lib/php/pear/PHPUnit/Autoload.php): failed to open stream: No such file or directory in /usr/bin/phpunit on line 43
Running which phpunit
returned /usr/bin/phpunit
Solved by more symlinking
sudo ln -s /usr/local/php5/bin/phpunit phpunit