Well, there's a simple solution. Make it bigger. This is a very old canyon. The average for the grand canyon is 10 miles. Let's make this 10 miles, and 500 miles long. Also, I don't think you multiplied by the number of layers in that one. We've got forty layers in the canyon. So, in the canyon itself, let's say we've got:

10x500x40= 200,000 square miles

Then, let's say we have, in addition to that, at least 10 miles on either side, for another... five layers? That's an additional

20x500x5=50,000 square miles

Now, let's assume we have enough caverns, that, were we to consolidate them, they would expand the canyon by 2.5 miles on either side. That's in line with other estimates of the caverns mutliplying the capacity of Ishka's canyon by 1.5.

2.5x2x500x40= 100,000 sq miles

Now, let's get an additional count of, say, 50,000 square miles for extradimensional spaces.

Now we have 400,000 square miles. That's saying that if we took Ishka apart and laid it out flat, it would be the size of California. I don't think that's a huge exaggeration (not, this is a rough estimate, I'm not thinking about creature sizes or types, and I'm not counting things like Mithral Heights that reaches far beyond the otherwise highest heights of the city.)

Now, with the figure you gave for Tokyo at 15,143.7 per square mile, I say Ishka could have a population of over six billion. Now, that's probably extreme, now that I've done all the math. But, even if we just applied the correct 40 layers to your calculations and said the lake district only had one layer, we'd get

(400x5x40)+(5x50)+(400x20)=88,250 sq mi for the main city
2x88,250=176,500 sq mi for the total city
176,500x15,143.7=over 2.5 billion
not counting Galdren, which is sure to have a few million