First - very nice job Ken.
As to glue and ipe- yup it is a bear to glue. Two things work against you here - yes it is oily, and also it is, as you know, very dense. As such the glue has a hard time penetrating pores to make a good bond. You will hear a lot of stories about ipe/glue failures, but these are mostly people trying to use glue as a structural bond, which is not your case.
If you were to need to replace plugs keep some ipe scraps around. I would really recommend using a tapered plug cutter (Veritas makes really good ones, though there are some Asian knock offs coming out on the market now). Second, to re-glue get the strongest non-polar solvent you can find and clean all glue contact surfaces. Toluene or xylene would be preferred, though acetone works in a pinch. Forget alcohol. Make sure you give enough time for the solvent to flash off before applying your glue.
As to glue choice, Fine woodworking test strength/failure of various glues on a variety of woods, including ipe. Though convential wisdom is to use epoxy or Polyurethane (ie Gorilla glue), the strongest bonds were made with Type 1 PVA (Titebond III). This will give you water resistance on the glue joint as well. I would let the re-glue set up for a couple of weeks if at all possible before re-applying your finish to allow the glue to fully set.
Again, nice job - you can see a lot of attention to detail there.
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