Any chance of looking at the ~$4 billion spent to date on Union as sunk costs (the government's had plenty of those lately... Power plants among others) and just rebuild the whole thing?
Close the station (tracks and all), maybe with minor allowances for through movements and brief stops for 5 years and reopen it looking like a normal 21st century transport terminal. The current Frankenstein station is outdated and dysfunctional before it's even opened.
When Madrid went about modernizing their principal train station (Atocha) they closed it for years. It reopened with two new levels of tracks and the capacity required to move Madrid into the 21st century.