Can't Find Further Documentation on Spartan3E IO
What about Spartan-3 Generation FPGA User Guide (UG331)?

1.:
Blank pads might be other pin types e.g. VCC, GND, JTAG, ...
Note that unused entities are not labeled.

2.:
Big chips use 2 or more coordinate systems.
- Pad107 overall pad number
- P98 pin number (pin 98)

3.:
A tile is a sub-region.

4.:
DIFFM means differential master.
DIFFS means differential slave.

5.:
RPM = Relationally Places Macros
You should check your documentation for relative placement rules and so on.