I had a MDD for some time, and it was/is a good rugged Mac. It is particularly noteworthy in having three separate ATA buses and three separate drive bays, the default bus for the boot drive is the 100 GHz bus that serves the drive bay near the power supply at the back of the chassis. The 66 GHz bus drive bay is located below the optical drive bays and forward of the 100 GHz bus drive bay. The optical drive bay is located at the top front and served by the third ATA bus which is 33GHz.
Logic and common sense would seem to indicate putting both the first and second internal drives in the faster 100 GHz drive bay, but logic and common sense are, in this case, wrong. Drive system performance is optimized by placing one drive, usually the normal boot drive, in the 100GHz bus drive bay and the other in the 66GHz drive bay. The secret is minimizing contention on either bus improves disk I/O speed noticeably. At least it did on my MDD. On this model Mac you should also configure the ATA drives as "bus configured" rather than master/slave. I don't know that improves performance, but it definitely improves reliability.
You have maxed out the RAM on the MDD so about the only other major speed improvement you could make would be an upgraded CPU, but those are getting hard to find. I just went to my favorite source and they no longer list upgrade CPUs on their web site.
