I need some help to decide which spherical keys should be from row 3 and which should be from their native row.
All alnum and punctuation keys should be from their specific row (1-4). Some modifiers do not exist in the rows where they would be needed.
Also, the space bars are all from row 3, so bottom modifiers would be better from row 3 too. As a side-effect, they would be more thumb-friendly.
I recommend to do all fuction keys in row 3, because they are usually not touch typed anyway and it would allow more flexibility.
2 units keys are not available in row 1 anyway, so row 3 is the best choice for them.
What about cursor keys? I'd prefer them from row 4, but on the other hand, they are kind of function keys.
Because we will save some function keys, I could add both variants.
Another question would be what to do with the numpad?
First, just to make sure that I understand how you are numbering the rows. Are you doing 4-4-3-2-1-1 from bottom to top? (i.e. the opposite way from how WASD keyboards does it: http://www.wasdkeyboards.com/index.php/products/individual-blank-keycaps.html
Which modifiers are not available in the rows where they would be needed? Without knowing which ones are missing it's hard to say exactly what I think would be best.
What do you mean by function keys? Just F1-F12 or everything like Shift, \|, backspace and such? In any case, I think that they should all stay in their native profile where possible and just have one or two that are not right. I don't know just how many would be wrong though, you'll have to tell me which ones are not available.
For the bottom row modifiers row 3 would be fine to match the spacebar. At least they will still be inclined the same way and who knows, maybe that part about being more from friendly will be nice. I wouldn't mind them as row 4 either though and just have the spacebar wrong.
I think all the modifiers, spacebar, shift, enter |\, backspace, etc should be row3. The numpad should be flat also, I really like the numpad on my olivetti, which in done that way. It sort of helps when typing in numbers.
For people who want to remap their caps lock key to either control or backspace (me! For Colemak! Even if you don't use Colemak you really should try using backspace instead of caps lock, it's fantastic and I got some of my Qwerty friends to try it using a simple registry edit in windows) I really think that the caps lock key should be the native row. It would be weird for me to have Caps Lock and "A" next to each other at different heights because I use the pinky for both of them and use both quite often.
Why is it that you want all these keys to be row 3 though? Why not keep to the standard row profiles where possible?