Thanks for the picture,
I see nothing wrong with the jumpers other than "D" should be removed to have no wait state ram(if its 60ns ram,remove it).
this would no affect anything.
Are the Amiga motherboard jumpers set to EXT?
even if boot delays were set and luns scanning on it still wouldnt take that much time.
I am using the warpengine in a A4000 with scsi card reader and full device and lun scans and it is still pretty quick.
Its a perplexing problem you have there.