I believe the old highway 4 from the Bypass to the Gold Country will remain the same route. The J4 Byron ~ Tracy will or has already become Highway 239. This is still in it’s infancy but will eventually be a four lane highway connecting Contra Costa to San Juaquin through Mountain House. The theory will be that E-Bart will follow on the side of Hwy 239.
However, today it appears to be an abandoned railway with a substandard patched 2 lane road next to it.
Of course this could all change