Lori,
The biggest gotcha was the "Trigger Files". JDE wasn't quite ready with all the known trigger file problems.
We do a SAVLIB with a save while active and we have had some problems with V5R1 and the QZDASOINIT's ending completely, thusly causing the save to fail.
The upgrade from V4R4 to V5R1 took about 6 hours on our AS400 - 9406 S30 (4way) with 4GB memory and 150GB DASD.
From the IBM standpoint it went pretty smooth. From the JDE side it took us about 3 weeks of various activities to settle down.