Migration Assistant from MacPro to new iMac

Just received my new iMac with OS 10.9.  My old computer is a MacPro purchased late 2008 using OS 10.6.8.  What is best way to transfer everything to the new iMAC?  The Mac Pro has USB2, Firewire 400/800 & Gigabit Ethernet.  The new iMac has Thunderbolt, USB3 & Gigabit Ethernet.  I have a Thunderbolt to FW800 adapter so can I use that connection for Mirgration Assistant or should I use the Gigabit Ethernet connection.  Just concerned my cable for the Ethernet connection is not current.  Also concerned that don't have same problem as couple years ago when did the Mirgation Assistant from an older iMAC to a new iMAC for my wife.  Some files didn't transfer and also Permissions were totally messesd up as later when tried to recover a file from Time Machine I kept getting message that "did not have permission".  Thanks to Apple Support I finally found a solution for recovering the file.  Haven't turned on the new iMAC yet as want to make sure I do the migration assistant right - No thanks to the manuals Apple now includes with new iMacs.    Thank You for your help.

I got everything transferred to the new iMAC following Pondini's article Setup Assistant tips  mentioned above by rkaufmann87.  Thank You.  Went to the section  "Problems after using Migration Assistant" and sub section "Fixing a UID mismatch after using Migration Assistant".  Generated temp user accts, logged off all accounts and then logged on the Temp Admin user acct and deleted all other user accts.  Then restarted iMAC and did the update from Time Machine disk from older MacPro.  Then logged off the Temp Admin acct and on to the account transferred over from the MacPro.   Best read the article to get all the details.  Then had to change names etc. to make them different from the old MacPro.  Still trying to get that straightened out.  As far as I know Permissions are OK. 
Now the iMAC power on is VERY SLOW.  Takes 3 min 20 sec to start up, even with all external devices disconnected.  Also having other compatibility problems.

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