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I run all three. I wouldn't run the GFO while the pellets are colonizing. After your pellets are fully up to speed, check your PO4(Hanna), and use the GFO if it's too high.
How old is your tank?
I would bring them on slowly, about 1/3 at a time, and add another 1/3 every other week, while measuring your N's and P's. I would use 1 cup at a time, and stop at 3 for a while. I wouldn't fill the reactor more than half way, with the pumps off. Set the flow so the pellets are just fluidized...
Yes, I would take the GFO off line, while the pellets are colonizing. I kept my GAC running. I also removed what was left of my Chaeto, since it would be competing for the same nutrients, and the pellets should be kept in the dark.
How much Alk are you using? The normal uptake in a reef tank is about 7ppm Ca to every 1 dKH Alk, given the margin of error in these test kits, it may be hard to notice that small of a change. Have you gotten a second opinion on the Ca reading?
Looks great. As far as the skimmer, you might take a look at this one, @ $265 it's probably one of the best investments I've made, and with a Sicce PSK 1000, uses the same pump as the Diablo's.
If I were to go back to t-5's again, I'd go with a 6 lamp dimmable fixture.
http://www.marinedepot.com/ATI_48_Inch_Dimmable_SunPower_T5_High_Output_Fixture_w_Controller_48_Inch_T5_Fluorescent_Light_Fixtures-ATI-UZ3313-FILTFIT58U-vi.html