UPDATE:
It looks like I've got a fix for problem #2. WD's Level 3 support guy was really helpful and provided me with the latest firmware (01.01A02) for the Se drives. Now, when I hit a single WD drive with two long read ops, the drive deals with it very well. If I start both read ops at the same time, the drive struggles like before for about a second or two (with a little of the growling noise) and then quickly (within about 4-5 seconds) ramps up to 170 MB/s. If I start the second read op after the first one, it skips the struggling stage and settles in at around 170 MB/s. I'm still testing to make sure that this firmware didn't make a huge sacrifice in other areas to improve multi sequential read performance but so far it looks really good.
I'm still working with LSI on problem #1 (controller doesn't read from both drives when it should).