Working through the posts in reverse.
Slot lengths
A slight difference in slots is common. 0.015 ? I don't know. Go ahead and see if there is anything to see. Flashing from the machining is possible, slight tweak to the throttle blades?

My gut reaction is if nothing obvious, Leave them the alone. A person with lots of experience and skill in tuning the low speed might teven them out by extending the slot or chamfering the blade. But if they are made longer it will make tuning harder. Then the blade may need to be shut more which will result in more slot above the throttle and everything may need to be redone (idle air bleeds and idle fuel restriction).

If you want to make a little more even, first measure the width and total length of both. If the shorter one is wider, then leave it alone. Area under the blade will be similar.

Initial Position
Anywhere from 0.020 to 0.035" of the slots showing under the blade will be correct on an older Holley like this. There is no exact magic number. There is no exact magic shape.
WRITE a note to yourself of how much the idle speed/throttle screw can be turned from .020 to .040"
This is the adjustment range you can work with while tuning. With this particular carburator, the upper limit with be the port for the timed vacuum. It must not be exposed at idle.

Secondary Slots
They vary depending on the carb and application. On a carb with idle mixture trim screws on all four barrels, some secondary transfer slot may be exposed. On a carb like the 3310, the secondary slots are pretty high up. The secondary idle circuit's job here is to help insure good fueling when the secondaries start to open.
It's best to leave the factory setup. However, if there is need to get a bit more air in at idle, cracking them a hair more open is one technique supply the additional air needed.

Side note about TMP
The pictures are nice but be careful with anything from Troy! He has some good info but some bad info too. Worst - he won't acknowledge what he doesn't know but will argue ad infinitum. It got so bad he was tossed from Speedtalk forum... that takes real effort.

Timing
Let's work with what you have. Yes as you figured out, because of the vacuum port exposure, the initial timing was not quite the same as what was set. If you want to try 18 initial instead of 16 that's fine, even 18. The important factor is that it is stable within the idle rpm range. And of course, that it starts easily both hot and cold. (Too much initial timing can make starting more difficult.)
You should find that increasing the timing at idle will allow the motor to idle with the throttle blades more closed than you had before.

edit: The idle mix trim screws will probably have to be adjusted each time a change is made to the throttle position.
The engine should respond to changes in the mix trim screws.

edit 2: The engine will not ping driving around at 38*. That's a good test for top end but needs to be done under full load 3rd or 4th gear at wide open throttle. Coke wants to register the vehicle, so wide open throttle can be dealt with later.