It's doubtful that the intake is causing this issue, unless, of course, there's a vacuum leak somewhere in that area.
I also doubt it's a DME issue, but you can rule this out by unplugging the battery for a while. I think 15-30 minutes will do the trick. Need someone else to chime in and verify this, but because our cars are so electronically "involved", it's definitely a worthy troubleshooting step. The DME itself hasn't changed, so a DME won't just one day decide to make the car buck...
This sounds like a potential fuel pump issue as well, though there may be another issue due to the codes that were read. One thing that can affect both banks 1+2 is a vacuum leak; check the lower intake boot for cracks (might as well check the upper one as well). This is a very common issue.