Just picked up a 09 rocker 6000 ks rode the bike home and was running well  
That night removed the baffle next morning took it for a ride and sounds a lot better and improved the pickup a little but when I decelerate it all turns to shit, coughs, pops, gergles very unhealthy   
I have also ordered a new air filter from yanky land. I will put the new filter on and then take into the hog shop for a tune up..... 
 

Will a tune from hd mob fix the decel problem ? 

need a tune ,would think so,! thats a huge baffle, So its straight thru ? I recon at least drill out the baffle a bit & put back in to be safe unil you come up with a better opion

I'd put the baffle back in the way it's supposed to be to provide some backpressure and have the sound at a loud but reasonable level. And that'd fix your problem. But bike will need a tune when the air filter goes on anyway

mate, well done, riding that thing back from WA.

In all honesty your going to need some form of fuel correction system (SERT, Thundermax, Power Commander etc etc) if your going to run with a free flowing air filter - like the one you have, and a set of pipes with no baffle. With no baffle / backpressure its always going to sound loud but run like chit at lower rpm although a proper tune will help iron out the main issues. mind you once you get up the rpm range she should start singing!

It may be too loud though and become a cop magnet

The air cleaner element you have is a cleanable type. Doubt it required replacement, just cleaning.
No baffle will result in no performance and the cough/splutter/ backfire stumble you're experiencing. It's meant to run a baffle.

Ask the previous owner if they had any tuning device, box, etc., or if it was simply download flashed by a dealer.
Basically as tussuck said.

Probably more important to change all the oils before you go bombing around, and check the belt tension, if it hasn't been done already.
 

Thank you 

+1 on changing the oils......NEVER ACCEPT what the prior owner says about the fluids. For $60 or so you can have peace of mind that your starting from a clean slate.