A description of the proposed improvements to the Gilroy-Salinas segment is contained in an EIR posted on the TAMC
website. The nutshell summary is that the bulk of the money will be spent on stations and rolling stock and only minor improvements would be made to track itself. An earlier plan for this project, dated 1993, indicated that the average speed would be around 40 mph between San Jose and Salinas. Given the meager trackage improvements listed in the EIR, it's probably safe to say that 40 mph would be an upper bound estimate for this latest plan.
I should also note that this project is contingent on $30 million in FTA New Starts money coming through. That's never a sure bet, although TAMC is about to impose a Regional Transportation Fee for new development projects in Monterey County that will add to the funding options.
The skepticism by Caltrain is perhaps the most significant obstacle at this point. Reading between the lines, it seems apparent that they have some significant concerns about the viability of this proposal and will probably place a lot of conditions on the project that will require TAMC to pony up a lot more money.