I agree fully that it is daunting at first. And if there's no experienced techs in your area, then it makes it that much harder.
But the manual is genuinely your best and most faithful friend. And you've also got an MRL tape which is vital for setting up proper flux levels in repro so that once set, you'll be able to set up the bias, levels and EQ to that fluxivity standard that your recording tape, (456, 499, GP9) will give you. The test tone generator on your mixer is not a replacement for that. It's for other stuff like I outlined in my previous post and only useful if it outputs the correct voltage.
So the basics of it are setting up the mechanics first, to know everything is mechanically aligned, then to get the correct input levels, then to set the VU and peak metering and then to move onto to repro settings to serve as the base reference for your record levels. And always in that specific order only. Once all done, simplified steps like just the MRL tape and a quick record level tweak will keep things consistent.
Also keep in mind that the machine is pretty stable once set and does not have to be constantly messed with. But do it right at least once and then you'll have less headaches down the road.
About your channels 12 and 13 not showing any signal, try jiggling the cards left to right a little bit to see if they kick in. Card connectivity issues can be a common issue with these decks and dead relays are also common service items. If you're going to re-seat a channel card, (un-plugging and plugging back in), power down first! Also, never attempt to calibrate the deck cold. Turn it on and let it warm up for at least 30 minutes to let the circuits stabilize. Again, all of that too is in your manual.
Also, treat that MRL tape like gold. Keep it away from all souces of magnetism and never play it on a dirty deck. Clean the heads first!!!!!!!!!11!
Cheers!