A spate of over 400 smashed subway windows in four months has the MTA on the verge of a glass shortage, transit officials said Friday. “We had a reserve of glass when this wave started in May. We’ve run through the reserve,” MTA spokesman Tim Minton said of the rash of vandalism. Since May 14, transit workers have reported 31 separate instances of broken windows on the 7 train, internal records obtained by The Post show. Smashed windows have also turned up on the 2 and 3 trains, MTA safety exec Pat Warren said — costing the agency more than...