As I see it, there are two related but separate questions.
Q1. How much current can the PS3 outputs safely deliver when configured in the soundset for the chasing mode.
Q2. How to configure and mount 40 LEDs - loose LEDs, pre-wired LEDs, LED strip, LED rope, fiber-optics, fill-in-the-blank, etc.
1. As the MTH service techs have not volunteered a spec from a service bulletin or whatever MTH supplies them, I don't think this info is forthcoming. The most useful info to date is anecdotal in that one engine was observed to parallel 4 LEDs. As mentioned, I think the best approach is to find a PS3 EVO and see how they did it - specifically if there is additional electronics to buffer the LEDs. But if that's not in the cards I would not try the destructive, add-load-till-it-fails test. As GGG points out, the PS3 LED outputs are different in that a PS2 transistor that drives a lamp output is repair-able/replace-able whilst the PS3 microchip that drives a LED output is not. If one had suitable measurement tools, the output capabilities of the four chasing outputs could be estimated. The idea is to watch how the voltage/current at the output change as you vary the load. But the procedure is somewhat tedious and is complicated by the pulsing of output.
So what to do. Well, are 10 LEDs in parallel plus a 300 ohm resistor in series bright enough?
There is some simple back-of-envelope calculation that suggests you can lower the 300 ohms to safely boost overall brightness. Consider that a typical LED driven under nominal test conditions looks like a 150 ohm resistor. That is you put 3V across it, and it draws 20 mA. V=I x R. So R = V/I = 3V / 0.02A = 150 ohms. So we know that the PS3 output can drive a 150 ohm resistor. By installing a 300 ohm resistor, you are guaranteeing the PS3 output will see a lighter load than even a single LED. The takeaway of course is, in lieu of finding the exact MTH PS3 EVO hookup, adding a spot for the series resistor is the thing to do.
2. Since even the manufacturers are not accurately modeling the prototype lighting, it seems up to you as to mounting method. Just my opinion but the idea is to simply show-off the chasing lights and changing sequence for charging vs. discharging. To that end, whatever gets the job done. If the spacing is not exact to the prototype, or not mounted at the right angle as to the prototype, etc.. then oh well. I still believe that you want to employ some method that does not require tediously routing/mounting 40 pairs of loose wires - in other words some kind of strip, bar, whatever that pre-positions many LEDs and can be soldered/assembled/tested on the bench before installation to the chassis.