CWP to CWP Migration - Convert Domain to Account

Ok I moved an account from another vps to my new vps. This account had several accounts under it because originally they were on a cpanel shared hosting. Anyway the move went great but when I went into the domains list and tried to convert a BIG site to it's own user account I got this and now I don't see the account under domains, it's now under users but it's not complete.

504 Gateway Time-out cwpsrv

So, my question is, how do I get this account to grab the whole thing without timing out???