If you are just trying to change the gearshift change rod it is fairly simple. There are two covers that you will have to remove, the clutch cover and the small cover on the right hand side underneath the front sprocket. The gear change shaft is held in place by 2 e clips on each side of the motor remove both of them and it will slide out of the right side. Here is a link to some diagrams that will help.
http://www.2wheelpros.com/oem-parts/2003-triumph-speedmaster-engine-cover-s-assembly.html
http://www.2wheelpros.com/oem-parts/2003-triumph-speedmaster-gear-selectors-pedal-assembly.html

2006 865 Neon Blue/Jet Black Speedmaster,790cams, TTP Stage 2 Firestarter, Epco Exhaust with 10.25" Samson Vrod baffles, UNI pods with 40 pilots, 150 mains,Thruxton needles, 3 turns out.