The manual seems to skip things and doesn't go step by step.
Everyone agrees the manuals for these scanners are junk. But even so it would be very difficult to provide a step-by-step for every type of system and situation.
I have found a trunking frequency. Its Motorola and when i tune the scanner to that frequency under the Motorola mode, some numbers pop up "MOT:XXXXX" then it goes to "MOT: none" and repeats with different numbers. I even tried inputing the numbers manually to the systems I want to tune to with no luck. What am I missing?
It sounds to me like you have found a VOICE CHANNEL. With regards to programming a Motorola type TRS in a PRO-164, that is of little use. What you need is the CONTROL CHANNEL. As mentioned it sounds like a Diesel; I think it is more like a buzzsaw.
Program the control channel frequency in to a bank (pick a bank). Set the bank to MO as well. Set the bank to OPEN. Press SCAN. As TG ID data is sent over the control channel, the scanner will automatically select the voice channel and let you hear the analog conversations.
Note that when you find a control channel, have it programmed in a regular channel slot (such as channel 0 0 0), have it set to MOT, and are parked on it so you can hear the buzzsaw; the 4th line of the display should display "MOT: Control 99%" (or some value), the TG IDs being used and periodically a System ID.