this paragraph is a little hard to read / understand. - genuine advice here, but perhaps take a little care with writing your paragraphs, as it can make it hard to understand, and hard to offer good help.
1. Have you tried clearing all the fault codes? - codes can be stored. I have an '08 as well, and when I first got it, I went into diagnostic mode, and found there were some codes already there.
I'd suggest clearing all the codes for a start, if they don't come back, then they are old stored codes, and are not contributing to your current issue.
If you dont go in and clear them, they remain stored, so this should be a frst step.
Once you have cleared the codes, running it for a while, then looking to see if they have come back or not, will tell you whether or not those codes are part of your problem.
2. The second thing I would look at, is possibly borrowing, or buying a power commander from someone else. You need to do this because with a 3/4 system (removed cat, and pipes) the bike NEEDS a power commander (or a flashed ecu) to run properly. If your power commander was not functioning correctly, then the codes may be related to the bike recognizing that the tune was wrong.
Basically, a poorly functioning power commander, or, no power commander at all, will cause the bike to run poorly - either of these things could contribute to the bike throwing codes.
After having checked the above, there are lots of other small things that can be looked at, but I think those are a good place to start.
You could also put the power commander back on, and go to the nearest shop with a dyno, and have them do a couple of runs, so you can see what the AFR looks like, as this might be helpful as well.
One after - thought - this is something that happened to someone I know with a 2008.
If you open up the airbox, the bike has got velocity stacks that lift up and down depending on RPM. they sort of clip into a little mechanism that lifts and lowers them at the appropriate RPM. If someone has done some work on the bike, and failed to clip them in properly, or if they have wiggled out - ths causes problems with how the bike runs. This will take you 15 minutes to whip the tank off, and take the top of the airbox off, and check.