mechanically they are the same, but asthetically they are different. mk2.5 has better looks, better instrument cluster, radio, red LED's inside, better centre console arrangement. most of the mods i have done are already there on the MK2.5 (spoiler, 17" alloys etc)
Method 1 is probably the safest, myself i do method 2 because i don't have a good clamp for the brake hose
Ive heard that pushing the piston back without clamping the hose off could damage the master cylinder as the seal would be going the opposite way and could cause it to bind, but i havent had any issues
for the EGR, blank it is the way, most users here have done it and there are only benefits. the only downside would be that the car would take a little longer to warm up because its no longer getting hot exhaust gases through the intake, but the car takes long to warm up anyway so you probably wont notice
the thermostat housing is the housing right in the middle of this picture: its from the MK2 but it should look similar.