Could my hypothalamus be giving orders to the adrenals to produce a surge of cortisol in response to my myasthenia gravis?

Yes. The hypothalamus will stimulate the adrenals when there is any physical, mental or emotional stress. If the myasthenia is symptomatic, that is a stress and could stimulate the hypothalamus.
Hypothalamus. The hypothalamus does produce crh (cortisol releasing hormone) which stimulates the pituitary to produce acth (adrenocortical hormone) which tells the adrenals to produce cortisol. An endocrinologist could work up this pathway to see if this is at issue.