Hello Eric,
Congratulations on the AT-11 project. It is my favorite Twin Beech. If you need any help with anything just ask. I have parts, blueprints, manuals, service information pretty much everything you need for the AT-11 and Twin Beech.
The panel looks great as it is rare to find such a stock panel these days. For what it is worth a couple of the holes marked for repair are stock or have a military connection to them. Here are a couple of notes about that:

A: these two holes are factory holes. The one at the bottom of the clock cut out is for an early clock that was not used very much but the cut out remained through later production panels.
B: These holes were for the landing gear control switch modification or Technical Order issued by the Air Force. In the before shot of your panel this mod plate was installed. It was done because of the high number of incidents where the pilot pulled the landing gear up on the roll out after landing when he thought he was raising the flaps. The flap and gear switch were identical AN toggle switches right across from each other on the throttle pedestal. It was easy to get them mixed up and they often did. The only difference between them was the switch guard was inverted on the flap switch. The fix was to move the landing gear switch up to the top of the panel to get it away from the flap switch. I can't recall the specific date of the TO modification so I can't recall if it was a WWII mod or not. It is interesting that the gear and flap position on later Beech 18's including the military aircraft remained at the original location on the pedestal but they changed the feel of the switches by adding a round wheel type of handle, like a tire, to the gear and typically made a flap like handle on the flap switch which is pretty much standard today.
About 10 plus years ago a gear up incident in an AT-11 on the roll out happened because of the identical switch problem so it is certainly still possible if you don't pay close attention to what is going on after landing. The need to keep an eye out on roll out to keep the Beech straight is sometimes greater than the need to see what switch you are reaching for and that can lead to expensive results.
So even though this is not a factory original mod it does have valid military history. Food for thought on the operation of these older model Twin Beech's.
I will be happy to look up and send you a copy of the TO on this if you like.
Please take a close look at your spar as there are some other Air Force mods by Technical Order that could affect the airworthiness of your spar. There was a gusset type of reinforcement done in service that can open up the spar to the atmosphere. They drilled holes through the spar and mounted gussets in the slide tube cluster to beef up the area because cracks were showing up from hard landings and high takeeoff and landing cycles common to the AT-11 bombardier training operations. Several surviving AT-11's have had this mod and the problem is if moisture gets inside any of the spar tubes then you could have internal corrosion issues. Some corrosion can be repaired but it all depends on the severity. Please check into this early in the project as it can be critical to the restoration plan/cost.
I have made a web page about this so for more information check this page:
http://twinbeech.com/beech18sparconcerns.htmI recommend getting an x-ray done early in a project like this so you can be sure that the spar is in good health or you can find out what needs repair work. I brought an AT-11 home on a trailer for a customer that had this spar mod. It turned out that the spar had water inside and it had rusted out the truss from the inside. There were holes that had come through the spar near the fuselage. If this plane had been flown home then the spar would have failed in flight since it didn't have a strap. This is an extreem case but is still a big concern on the older Beech 18's and all of them for that matter. I don't want to scare you as spar problems on most Beech 18's are still rare but they do occur which is why this should be looked at real early when ressurecting an airframe that has been sitting for a long time.
Please call me any time as I am always happy to talk Twin Beech especially AT-11.
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Thank you!
Taigh Ramey
Vintage Aircraft, Stockton, California
http://www.twinbeech.com'KEEP ‘EM FLYING…FOR HISTORY!'