Answers to your specific questions:
1. Arm system: To my knowledge, the Ike housing doesn't come packaged with an arm system. However, you can get the DS-125 in several packages. You can get just the strobe (but without the TTL sensor, it is useless in your application). You can get the strobe, sensor and arm. You can get the strobe, sensor arm and tray (for a housing w/o a tray). You have expressed interest in the Ikelite housing -- this already comes with the tray (6130.1 is the part number for the housing with one handle, I think you can get the two-handle version by ordering 6130.2; if not, you can get a two-handle tray separately if you want to). The arm that comes with the packaage is quite functional, though it isn't the most elegant thing in the world. Ike has updated the arm system so you don't have to reposition the sensor when you reposition the strobe. If you go with the YS-90DX and want Ike's basic arm system, I'll sell you mine for $20 -- you'd just have to make sure you fit the YS-90DX on the end (I assume it would work, but am not positive so we'd have to figure it out). I got the arm with the DS-125 package but already had a ULCS system.
2. With the Ike DS-125, I would highly recommend the fast charger. Other than that, no accessories needed. For the YS-90DX, I would recommend the fiber-optic cable and AA NiMH batteries and a charger (about $33 for four batteries and a reliable fast charger, more for a better (e.g., Ansmann) setup).
3. Prices: I surfed over to B&H Photo Video (one of the reputable online sources and a good place for realistic pricing) and determined the following:
YS-90DX:$479.95, fiber cable $58.50
DS-125: strobe, arm, sensor package $649.95 (but out of stock), rapid charger $109.95
4. Battery door on the DS-125 is completely different than the 200. The 200 actually has a "door", the DS-125 doesn't. The rechargable battery on the DS-125 is a separate piece and connects by a pull and turn, key-lock kind of system (e-mail me for pictures). It is very user-friendly. Incidentally, because it is designed this way, you could have an extra battery pack ($106) and have it on the fast charger while you were underwater with the strobe (and, obviously, the other battery).
Mike Oelrich