If the emergency disk says "invalid resident library" then it has nothing to do with partition size. The emergency disk boots from CD, it does not need the harddrive.
Make sure you have the right 680x0 libraries installed. You need a small 68040.library (ca. 700 bytes) and a big 68060.library (ca. 100,000 bytes).
Also the 4GB problem only applies to the internal IDE controller. If you have a SCSI disk and use SFS you can use partitions of any size.
