MircoNewbie, Alban has answered all your specific questions but if you want to extract the information yourself, here are some pointers that will help:
Chapter 1 describes the overall function of the chip. It contains memory maps which show the on-chip and off-chipmemory and a block diagram which shows the features of the chip. If you are interested in a specific feature like a timer look at the block diagram and see what timers there are.
Appendix A contains the electrical specification of the part and that is where you will find operating frequencies etc
The remaining chapters give full details of the modules of the chip. You need to read these to understand how to use them.
You are asking a lot of questions about the CPU. The S12XE has two CPUs. One is described in the data book and is called XGATE - look in this chapter to find out about its instruction set and programmers model. The other CPU is described in a separate book called the S12X CPU reference manual.
If you are new to this device I strongly recommend that you read some supporting material from this website. There are short documents called product briefs that give introductory information about the products. There are application notes that describe features of the architecture and how to use the part. You can find all of these documents by searching for S12X on this web site or by looking at the product pages for the S12XE.