Just what I thought - your internal drive is unterminated, hence the booting problems. Those three white slots under slide covers are empty.

Unfortunately, IBM choose to use the strangest form factor terminator resistor networks, that I haven't seen before. Unless you can find the right ones, solutions to your problem could be:
1) internal pass-thru SCSI terminator that goes between internal SCSI ribbon cable connector and drive, if there is enough space behind the drive, or
2) SCSI terminator that attaches to last connector on ribbon SCSI cable, but in that case you will need new internal cable with one extra connector
See:http://68kmla.org/forums/viewtopic.php?p=163005#p163005

Unfortunately, IBM choose to use the strangest form factor terminator resistor networks, that I haven't seen before. Unless you can find the right ones, solutions to your problem could be:
1) internal pass-thru SCSI terminator that goes between internal SCSI ribbon cable connector and drive, if there is enough space behind the drive, or
2) SCSI terminator that attaches to last connector on ribbon SCSI cable, but in that case you will need new internal cable with one extra connector
See:http://68kmla.org/forums/viewtopic.php?p=163005#p163005