Hi, Karen - I would certainly not consider breeding Java if she were my mare.  Aside from her current difficulties, you had written this in her case history:

Until she is healthy and well, and you know for sure that she is neither HYPP or PSSM, I would hold off on breeding. The symptoms of horses with HYPP can range from no signs whatsoever, up to total inability to move. 

Another consideration is that pregnancy always worsens IR.

I appreciate that money is always tight (especially when one has challenged horses!); if she were mine, I would spend the money on the PSSM Type 2 muscle biopsy test, and the UC Davis hair test for HYPP.

https://www.vgl.ucdavis.edu/services/hypp.php

In the meantime, continue to treat her as IR (since she is); if you can afford to do the ACTH, get ACTH, glucose, leptin, and insulin; that is this one, plus request glucose:

https://ahdc.vet.cornell.edu/test/list.aspx?Species=Equine&WebDisc=&TstTyp=&Test_Name=acth

. The full metabolic panel includes thyroid, which you don't really need.  Primary hypothyroidism in horses is extremely rare, and secondary low thyroid due to disease states and dietary issues will resolve when those things are resolved.

Thanks a million for having your case history link!