Thigh muscles ache/twitch after flu shot 4 days ago. Took blood labs no abnormalities. Neuro test reflexes/strength successfully. Told to rest legs and drink plenty of fluids, in 2 weeks emg. Opinions?

Sounds accurate. Cannot imagine a neurologic reaction to flu vaccine except that there have been some cases of guillion-barre syndrome (a form of ascending paralysis) associated rarely with vaccinations. The recommendation you received is good as long as you follow up quickly if you are not getting better and definitely if you develop any other symptoms.
Flu shot pain. It is not uncommon for the flu shot to give pain for a day or two. However, from your description is sounds like poor technique was used when you were given the shot . I would suggest warm baths and pain relief in the form of ibuprofen. The pain should pass in a few days. An EMG is not indicated.