I only read the first half of your question because I think I know the possible problem after the first two sentences.
This should be your machine:
Apple iMac "Core 2 Duo" 3.06 24-Inch (Early 2009) Specs
Identifiers: Early 2009 - MB420LL/A - iMac9,1 - A1225 - 2267
Apple was just switching over to the proprietary Apple hard drives at this time that require specific Temperature sensor cables for each brand of hard drive. At least they did with the late 2009 machines. This may not be the problem at all but I think it's worth a shot for $8.50: http://cgi.ebay.com/IMAC-HARD-DRIVE-TEMP-SENSOR-PART-922-9224-/160574699683#ht_500wt_1413
922-9223 Hitachi
922-9224 Seagate
922-9225 Western Digital