I am in the odd position of thinking that the sample texts in the answers given by Dale Hartley Emery and Thanasis Karavasilis both read well despite the fact that in terms of the advice given they directly contradict each other. *And* I thought that your original formulation was fine - in fact I liked it best of the three.

DHE is advising you to consistently omit all the insertions of "she thought" or equivalent tags and just go straight to third-person recapitulations of the character's exact thoughts. TK is advising you to consistently put them in. To me DHE's recommended style reads as slightly more fast paced and tense, at the cost of being a little less clear than TK's recommended form. Your original had a mixed style. Personally I thought yours was a happy medium.

You mentioned that "I get complaints from my readers that the text shifts POV."  Meaning no disrespect to your beta readers, but given that you sensibly started by explicitly notifying the reader to the fact that these are thoughts with the words "Her mind immediately flooded with panicked thoughts", I think you shouldn't worry too much. It was certainly clear to me what was going on. When it comes to clipped sentences like "Had he gone back to California already?" the "rule" that one must never shift point of view scarcely applies. Very short phrases or questions that come in a stream of thoughts aren't really perceived as having a POV. Even if technically there is a shift from the character's POV to an unspecified narrator's POV it is in practice obvious who is doing the thinking. It is the POV equivalent of omitting the personal pronouns in casual speech, e.g. everyone understands that "Seen Harry around recently?" is short for "Have you seen Harry around recently?"

I conclude, boringly, that there is no "best way" to do it. It is a matter of style and personal preference.