Cake – ny other difference between the cakes and the cup cakes besides the size

Firstly, it strikes me as odd that your recipe has no raising agent - no baking powder, no bicarbonate/baking soda, no self-raising flour. Unless you're whipping a lot of air into the batter, the cakes will barely rise, and you will end up with 'cookies'.

I would add 2 teaspoons of baking powder and 1/4 teaspoon of bicarbonate of soda (baking soda) and see if that helps.

As for the temperature of your oven, I wouldn't go so far as to halve the temperature and double the time. The idea is that you need enough heat for the cakes to rise at a decent rate then form a crust on the outside. 100 degrees will do little but slowly dry the cakes out.

Domestic ovens are rarely well calibrated, so your oven may be running hotter than the dial indicates. Invest in an oven thermometer to make sure you are setting the temperature correctly: I have had an oven run 40 degrees hotter than the dial said before now!

If you haven't got the time to get a thermometer, try setting the oven about 20 degrees cooler on the dial, to around 180 degrees.

I immediately thought of this table, from the front of the muffin section in Bread, by Beth Hensperger*:

Muffin size          Baking time     Yield
Mini/gem (1 5/8")    10-15 minutes   18-20
Regular (2 3/4")     20-25 minutes   9-10
Oversized (3 1/4")   25-30 minutes   6-7
Muffin cake (8-9")   55-65 minutes   1

The baking times are for 375-400F; most recipes will fall around that range. Note that the yields don't necessarily match up to typical pan sizes; for example, if you take a recipe meant for 12 regular muffins, you'll probably have more batter than you need for a pan of 6 oversized muffins. Similarly, if your recipe says to bake regular muffins for 30 minutes, you might have to bake miniature ones a bit over 15 minutes. "Muffin cake" refers to baking in an 8-9" pan of some sort - the author says that you can get away with it for any muffin recipe, but I've never tried it!

P.S. I know this is for muffins, but cupcakes are fairly similar, so I think it'll be about right!

_{* At least, I'm pretty sure it is. I have a copy of just this page (for the recipe next to the table, actually), from a book my mom has. I recognize the cover, I know we had that book, I think this was in it, and Google book search somehow found it when I searched for "fresh-lemon muffins".}