How did you verify you have no draw on the battery?
Did you remove the neg side cable and put a voltmeter between the cable and battery post? That should read zero or dang near it, but it should not have a full battery voltage draw on it.
Since your vehicle can sit a couple days and still start, you don't have a diode problem, because if you did, you'd have a dead DEAD battery by morning. I'm pretty sure the diode trio is one piece and impossible to install wrong. Diodes are not installed individually....anymore at least.
An alternator makes three phase AC electricity, and the diodes rectify that into DC. Each phase has a pos and a neg wave, and a diode is needed for each side of that wave, and with three phases, you need six diodes. If one diode goes bad, you lose one third of the power of your alternator, but more importantly you have a dead short that kills your battery as fast as leaving the lights on all night. Since you don't seem to have a dead battery, that tells me your alternator "SHOULD" be fine.
While I don't know EXACTLY how this system is setup, the principle is generally the same. The alternator will NOT start charging until the rotor is excited. It only takes a very small amount of power, amperage, to excite the rotor, and when it's excited, that creates the magnetic field that passes through your stator's magnets, and it starts producing your working power.
The light on the dash comes on when it's not charging, and that generally means the rotor is not being excited since it sounds like the alternator is working, just not right away. What causes that delay, I don't know for certain without looking at it, but if I was to venture a guess, and taking into account you're in the cold state of Wisconsin and it is winter, I used to live there so I know, and you say this happens after sitting a while, I'm thinking that "MAYBE" it's your battery.
The cold takes A LOT out of your battery, while at the same time your engine is requiring MUCH more to get it started. Then you have the electrical preheater going, and then you're cranking the engine, and all this takes its toll on your battery. Your battery voltage "MAY" be too low for that 45 seconds, to provide enough voltage to cause your regulator to excite the rotor, and start the charging process.
It may be that after your battery catches its breath, so to speak, for that 45 seconds, that only then does the battery voltage return to the level needed to excite the rotor, and allowing your alternator to start producing power. Until that happens, your dash light will be on.
What that wire is that the dealership added....that I would be asking them. If you do ask them, please come back and share what their reason is for doing this. I'm really curious as to what they say.