Conflicting Mail has both IMAP and POP

A friend called me earlier today because his iMac (2009) had run out of space on the main disk.
He had watched it counting down free space while he was doing nothing.
After digging about and clearing out Trash, I found that his Apple Mail was 136GB in size and that it had two accounts defined.  Both were his email address; once defined as POP and another as IMAP.  When Mail was open and in the foreground, one could see the "twirling clock face" (busy icon) beside both.
I deleted the IMAP account (he'd said he has nothing important in his mail) and the newly freed up space stopped counting down.  So that was a start.  I then thought we could reboot.  However, that was held up because Apple Mail couldn't shut down.   I suspect it may be unwinding whatever it had done.  I've now left it for the day and it's sitting there, doing lots of IO but not shutting Apple Mail.
Tomorrow, if Apple Mail hasn't shut down I plan a Forced Quit, followed by a reboot and Verify Disk.
Does that sound reasonable?
Is there a mode of starting Apple Mail where it might rebuild its mail?
After this, any suggestions on where I might find files that could be trashed?
136GB for Mail sounds gigantic.  (My own email, which goes back 9 years, is 8GB in size). 
Your suggestions will be welcome.

Force quit it, but first...
Open Console in Utilities & see if there are any clues or repeating messages, especially about Mail.
One way to test is to Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, Test for problem in Safe Mode...
PS. Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive
Reboot, test again.
If it only does it in Regular Boot, then it could be some hardware problem like Video card, (Quartz is turned off in Safe Mode), or Airport, or some USB or Firewire device, or 3rd party add-on, Check System Preferences>Accounts (Users & Groups in later OSX versions)>Login Items window to see if it or something relevant is listed. Or an errant process eating up RAM.
Check the System Preferences>Other Row, for 3rd party Pref Panes.
Also look in these if they exist, some are invisible...
/private/var/run/StartupItems
/Library/StartupItems
/System/Library/StartupItems
/System/Library/LaunchDaemons
/Library/LaunchDaemons
Mail can Rebuild a highlighted account by using the Mailbox menu item>Rebuild.

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