When you are using the SH9MD to communicate from the 4060 to an 1128, you are using the cable for SCXI communication. You are connecting this cable to the back of the 1128 and the only signals it can carry are SCXI communication and the Measurement Complete (MC) from the DMM to the Switch. The 1128 cannot route his Scanner Advanced (SA) signal to the back where the SH9MD connects, and there are not any available PIN to carry it.
If you want to use handshaking with a PCI 4060 and a 1128, you will need to control the Switch using a different controller than your PCI 4060 (another 4060/4070/4021) connected to the back of the 1128 using the SH9MD cable. You will also need to get the "trigger cable" for your PCI 4060 (available page 298 in 2002 NI catalog). This cab
le splits the SH9MD into 2 BNCs; EXT TRIG IN and MC. These BNCs need to be connected to the SA screw terminal and to the EXTRIGIN screw terminal respectivelly on the 1331 terminal block.
The DMM will need to be set to external for both the Trigger/Sample trigger and the MC destination. The Switch would also have its SA destination and input trigger set to "front of module X".
A very good source of information in the "NI digital multimeter help" available on the Web. Check out the Triggering section under the Programming heading.
Good luck.