First off, the Kickstart 3.1 roms will have a longer boot time than Kickstart 3.0 when no IDE devices is connected. An Amiga with a SCSI harddrive instead of an IDE drive tages ages to boot. 30 seconds isn't unusual.
Have you tried arranging everything as it was in it's initial state? Reinserting resistor packs (why you would do that is a mistery to me), Kickstart 3.0, etc.
Have you gotten some speakers plugged into the audipo outputs of the A4000? If so, does it give a buzz/tone when powering on (caused by the WarpEngine)?
