Eurofighter Typhoon excellent photos

Reference to photos in Post by TEEJ 17 June 2008 20:27
http://forum.keypublishing.co.uk/showthread.php?t=81778

My questions relate to areas on photographs (see attachments) which I have circled in green and they relate to the Eurofighter Typhoon (not to TEEJ’s excellent photographs) and my interest is in understanding correctly what I am seeing, primarily on the port side of this aircraft.

74e3F205_Ex1.jpg visible on port side

Ec491379_Ex2.jpg visible on port side

25eb34ca_Ex3.jpg visible on port side

393d074d_Ex4.jpg NOT visible on either side due to angle of photograph

.aa1cc213_Ex5.jpg NOT visible on underbelly

.e5e6e7fb_Ex6.jpg visible on port side

76514ac9_Ex7.jpg visible on port side

The only information I have found that may possibly explain the discolouration is the following –

http://www.eurofighter.com/et_ss_ss_sp.asp refers to “The Secondary Power System (SPS) enables the hydraulic and electrical systems, and engine starting. It consists of an Auxilliary Power Unit (APU) and two engine-driven gear boxes”.
Can anyone please either confirm (and if so why the exhaust type burn on an otherwise clean fuselage skin?) or please enlighten me if I am way out ?