I've been installing public safety radios for decades, and I can't emphasize enough what WD4JKH said about the green wire being connected to the same source as the large red wire. MaraTracs are especially sensitive to any voltage differences between these two points and bad grounds. Simplistically speaking, the internal power supply is not isolated from ground as in the more high end MotherMotos, and any voltage differences between the voltage inputs and between any ground points will cause undesireable effects.
You can tie the orange wire to any switched source if you want switched functions, but if switched functions aren't a priority, you can connect it where the green wire is connected. I have several UHF and VHF hi and low band MaraTracs in various vehicles, and as long as they're installed properly, they are one of the most reliable radios that were available in their time.
If you get alternator whine in the receive audio when unsquelched, or worse, if there's alternator whine in the transmit side, check the ground again. In fact, check for voltage between the battery negative, where you have the radio grounded, and where the antenna base is grounded. Ideally, they should all show zero differences. If you see more than a miniscule number of millivolts, you'll need to get that resolved because the circuitry will "see" the difference, and noise will ride on that potential difference in the circuitry. Over the years, I've found that the low bands are especially prone to any voltage differences between these points, but all are susceptible.
As stated above, make sure the VIP plug with the jumper is plugged in next to the mic input, or unless the internal jumper is in place inside the control head, there'll be no transmit. Need any more info, feel free to ask.