[Bfan]

If I understand what you are saying correctly, you used ROW Boxster flash for the DME. It will make the car run awfully lean with the 3" 996 MAF housing. The DME will think the engine is getting much less air than it really is and will adjust the injection of gas accordingly, i.e. the car will be running lean. I haven't studied your codes in detail, but believe you have 3 options.
1. Run with an aftermarket DME-tune from some of the reputable tuner that understands these things.
2. Re-flash with ROW 996 tune. (appropriate for the MAF house that you have in the car)
3. Run with the Boxster DME-tune and the original Boxster MAF housing.

Options 1 and 2 will understandable give you a little more power than op 3.

I believe that if you disconnect the MAF wiring, reset the codes with Durametric or by disconnecting the battery for 20 sec, the DME will revert to a "standard" mapping that it has stored and the car will actually be running a little rich, which is a much better situation, but don't run it for to long that way.
If you search this forum you will find that Byprodriver has written something on the subject.
My advise is to start up with new O2 sensors and fresh injectors if you want a smooth running, powerful engine. Don't ask how I found this out....
Good luck