The period(.) in 'tom.willis' seems to be throwing off the /etc/group file. Is there any way around this? I tried quotes, and escaping the '.' but to no avail.

You created the user with useradd, I assume. You can alter the group membership with usermod.

No I just modified the /etc/passwd, and it works great. I tried usermod -G apache tom.willis. It adds it in /etc/group but when I tried and execute php as that user I get a permission error on the file /var/lib/php since only root and apache group and create files related to session state in there. I could change the session.save path to /tmp in the php.ini but I'd rather leave it as it is. php works fine if I add a different user to the group, but for tom.willis, it's tricky.

I could add OTHER write permissions to the /var/lib/php but I'd rather not.