2000 cycles? That's strange. As far as I can tell, I set it to simulate up to 5 million reactor ticks, which if I'm not mistaken is 100 cycles for thorium rods, 250 for uranium rods, or 500 for MOX rods. I'm not sure how to count the cycles for a reactor that uses a mix of two or more fuel types, though. Edit: I noticed one possible source of confusion using your design: it says 1996 items are replaced in that duration, but since you had 4 dual mox rods, that's really only 500 cycles for them.
As far as replacing more than one component type, how would you automate that? I am not aware of any mod that would be able to do that properly. If you're manually replacing components, it seems to me that the simple cycle simulation should be sufficient to determine what it would take to get infinite cycles out of it (in terms of which components would need replacement and how long to let it cool down for).
For the pulsed cycle, I suggest you start by running it in the "single cycle" mode and look at when certain components (or the reactor itself) break, and start with the on pulse being a second or two less than that, and maybe the same duration for the off pulse. Then you can tweak them up or down to increase performance or safety. I don't know if Talonius's planner properly handled the heat exchangers, because I don't entirely understand them myself (as you might recall, I had to ask for permission to adapt the IC2 code for them rather than going by Wiki descriptions), but they make it impractical to use anything but a simulation run to predict when components will break.
As far as Talonius answering me, here's what happened: he hadn't replied to my private message, but I noticed his profile had a link to email him, so I tried that a few days ago, and he was fairly quick to respond (by email) with an explanation of his codes. If you look at post 68 in this thread, you'll see that I've already added support for codes from that planner.