1) Althou i sound unhelpfull , but the PDF is pretty straight forward to me. The casing , the flat frontal part and the indicator of the pins, should have given enought information to you to solder it.
Doesnt the PCI has any labels ? C (collector), E(emitter) or B(base)? If not, doesnt it come with a paper with the circuit schematic?
http://www.tpub.com/neets/book7/25b.htm
PNP and NPN transitors. If you've got an schematic, it gives you which is Base, Collector and Emitter . Just follow the arrow, literally

. Each transistor pin can be identified by the arrow.
> and the other one goes to a pin on the large transistor
Usually, it gives current to the base of the large one, and regulate the flow of current though the transistor .
2) What do they look like? (
reference).
If (2) then the 104 is the 100nF. Usually is Z and not M. Must be a voltage reference or similar. 101 it's an 1nF . Both ceramic.
You should have a (3) type one for the 100uF. Ceramic type capacitors usually dont go over 1 uF. The larger ones in the picute are 220nF and go up to 250v.