im planning on upgrading my exhaust system and ive decided on the exhaustb system above.. how hard is the process
of changing the exhaust .. would it be a big job for guy that knows what hes doing with all the right gear?

Should I replace stock manifold with some good headers while I'm getting the exhaust done? I've been looking at some headers on emspowered

No not worth it. They will only crack and cause hassles. 

I was thinking 2.5 inch with 2.5 downpipe , I've heard the 3 inch doesnt bolt straight in ...

pretty sure the 3" bolts straight in. Just need alot of fiddling near the aircon pipes to fit in. Don't replace the stock manifold. Most of them do crack. Fairly easy job just the rusty bolts might be a pain to get off. Spray them with wd40 for a day or so before you start the job. Makes it easier.