I'm not experienced enough to figure this out.
EXPERIMENT!
The best way to get that experience is to experiment! You CAN do it. But you have to try.
Without experimenting, you can't find out what is wrong. Even an expert needs you to help him or her figure out what needs to be fixed. About the only other thing even an expert could do is to use socks with built in pressure sensors, so you can see where the boot is creating extra-pressure points. Something a real medically qualified expert, like a podiatrist, t MIGHT be able to do, if he has the right hardware.
It takes a lot of time to experiment with all these things, if you don't know where to start, because you don't feel pain in any one place, but feel it all over. But I think it's worth it.
E.g., Try each of the following things. Does it make more or less pain, or do nothing? If each trial doesn't improve things, undo it (e.g., if it involves adding tape, remove the tape):
Investigate whether the boot is pushing down your arch by temporally putting strips of cloth athletic tape (sometimes called coach tape - widely available in dollar stores, the first aid sections of drug stores, sports stores, etc.) under the part of the insole under the arch.
Investigate whether it is pushing down the rest of your foot by temporally putting strips of tape tape everywhere else.
Investigate whether one side or the other of your foot is better supported by the other by putting tape under one side, then the other.
Since you had to punch out your toes, I doubt the front of the foot is sliding sliding side-to-side. But if the back of the boot is too wide, your heel could be sliding side-to-side. You could try adding tape under the heels that is too long, and wraps around your heels. You don't want it to stick to your heels - although I guess an alternative thing just for one brief experiment would be to tape the sides of your heels. Likewise you can figure out whether your foot is sliding forward and back by taping the heel, or the boot behind the heel. Abrasion due to sliding can cause pain - and sliding around makes it really easy to hurt yourself.
Investigate whether the boot is too small and/or or the insole too high by removing the insole. Is it loose enough for your foot to slide around, or for you to feel unsupported? Is there more or less pain? But be careful - some footbeds have sharp objects or poky bumps that you may need to put something like tape over, to avoid injuring your foot. You can also try thinner socks too. Some people use none, but I think you need a really good boot fit (which you don't have yet) to get away with it - though maybe you could cut a thin cardboard (or thick paper) insole to the same peripheral shape as your current one.
Once you have extra space inside, you have a lot more room to experiment with the other things mentioned here.
Maybe the heel is too high. I'm a guy, don't wear high heels, and that has been a huge problem for me. But even if you do sometimes wear high heels, your boots might lift your heels higher than you are used to. So try adding tape under everywhere but the heels.
Maybe the place your foot is bending upwards, near the front of the foot (ideally it should be right at the ball of your foot) is too far forward or back. One fitter told me the single most important thing in boot fit is quite probably getting the position of the foot bend right. That might not just cause pain - you could seriously injure your foot that way. Tape under a very thin insole can be used to reshape the effective bottom of the boot a little to move the bend point forward or back. Also, maybe it is bending your foot too much. So try taping across the bottom of the insole under the bend point, to reduce the bend.
Investigate whether the boot is too large by wearing thicker socks.
BTW, your socks should be higher than your boots! Wearing short socks is a really common mistake.
I'm not sure what you mean about the tongue being too wide. Too thin is obvious - if you can see your foot or sock, on any place below the top of the boots, it is too thin. The tongue should tuck under the sides of the boot, not above the sides, on almost any shoe.
But there are a few bad things a wide tongue could do. E.g., It could push down or inwards the sides of your feet.
In addition, it is really important that the sides of the tongue be "feathered" - i.e., that at the sides they gradually get thinner, so you don't feel a sharp edge. And in fact, you should not feel a sharp edge against your feet anywhere on the boot.
I guess you could do some simple experiments with the tongue, just like you can with the insole.
E.g., put cloth tape under the tongue in the middle, or on one or both sides. If the tongue isn't featured, you could stick tape around the edges to smooth it out a little. That would look ugly, by for now you are just trying to figure out what is wrong. (It is probably possible to sand the edges of the tongue to feather it, but that's a permanent change. Likewise, you can probably sand the sides of the tongue to make it thinner, but that's a permanent change too.)
I had a lot of troubles with my ankle bones. In particular, my fitter didn't specify to the boot maker where the bones were or how large they were - so even though they were custom boots, the boot maker didn't shape the boot to accommodate the ankle bones. If you feel a lot of pressure against your ankle bones (on either or both sides of the ankle), maybe they aren't punched out far enough, or are punched in the wrong place.
There are people who supposedly have trouble with excess pressure against the Achilles tendon. Maybe making extra space inside the boot, using the methods described earlier, would help? In the long run, if you were sure that was the problem, you can punch out the back a little - but that is one of the stiffest parts of the boot, and it would be hard to punch much.
Likewise, there could be excess pressure against the middle height parts of your foot. Insufficient pressure to provide support could be dealt with by taping, but aside from making extra space, it is hard to deal with excess pressure, except by punching, so it is hard to experiment.
I've heard a lot of good things from good fitters about custom Harlicks, BTW. But to some extent, there is little point to getting custom boots if you don't know what to fix.
One last thing. If none of the things I have suggested helps, you could have injured your foot. E.g., you could have a fractured bone, or something else. It's expensive, but it might be worth getting it checked over, before wasting money on custom boots. I don't know how to check for that yourself, but I guess, when you are not skating, you could try putting pressure on different parts of your feet, and bending your feet, and seeing whether that hurts. It's worth a try, but it would be better to have someone medically trained check it over. (I read somewhere that a medical team at the University of Delaware had concluded that most competitive figure skaters WERE skating with fractured bones, and I've heard something similar for a lot of dancers and other athletes, so it isn't completely impossible.) OTOH, since both feet hurt, you would have had to injure both feet for this to be the issue.