It's hard to diagnose wiring problems remotely, especially one-of-a-kind custom wiring. Photos do help. I'll try a couple of suggestions.
If you separated the two batteries, and one went dead in two weeks, it is possible that you no longer have a charging source for that one, and you simply "emptied the tank." Or if the bus was parked, there may be some instrumentation that is always on. I have a camper with an "always on" propane leak detector, and it will run the battery down over time if not disconnected or recharged.
As far as the flashing lights, I have two possibilities. One is that the mechanic wired them to the turn signals. I have found that a majority of good mechanics really don't understand wiring, which is not "mechanical." This would be a faster flash.
The other possibility is that the lights are powered through a self-resetting circuit breaker. These breakers are usually in a rectangular silver metal can with a black top, or in a black plastic block. There will usually be two studs for the hot and protected wires or buss bars to connect to.
If the two light sets together draw more current than one breaker can pass, either due to size or age, then it may trip and then reset and then trip and reset again. This might be a slower flash or have different off and on times. Use a meter or test light to see if the hot wires to the two switches go "cold" as the lights flash off. If this is the case, power the switches from separate sources
Self-resetting breakers are usually used for important circuits like headlights and windshield wipers that you need to safely get off the road. Occasional interruptions of excess power draw may prevent a wiring fire while you search for a safe place to stop. They also can save wiper motors when the blades are stuck in ice from freezing ran. Other circuits usually but not always have fuses or breakers that must be manually reset.
The voltmeter issue would have to be looked at. I am assuming you mean the meter in the instrument panel. It could just be how the indicator is wired versus the added wiring. Most vehicle meters are "damped" so they don't dance all over the place with instantaneous variations in what they are measuring. Instead, they move slowly to show trends as opposed to instant status. So something might have affected the leads in a way that would remove the sensing variation from the panel, either making the ground reference hot, or the hot reference low by drawing power away from the sense wiring.
On the other hand, something could be connected backwards that drains down the battery, and the delay you are seeing on the meter is the time it takes for the battery to recharge . . . . .
It really sounds like you might be drawing power for some of your wiring from undersized sources. Finding a good source can be tricky sometimes. My favorite "oops" was a professional radio installer who needed a power source in a semi tractor fleet that went on and off with the key. After a week or two in service, the dispatchers complained they could talk to their trucks fine when at delivery sites, but not going down the road. It turns out the installer had wired the two-ways to the brake lights.
Someone said "Making good decisions comes from experience, experience comes from bad decisions." I say there are three kinds of people: those who learn from their mistakes, those who learn from the mistakes of others, and those who never learn.