Check also C1, C7, C12, C13 which are also +5V bypasses to ground that you probably recapped (47uf/16V). There are also a ton of .1 and .01 SMT caps on the underside that bypass +5v, however these rarely short unless mechanically disrupted.
The recapping process involves a lot of board handling and soldering which can scatter bits of solder, broken pad and trace copper, capacitor lead clippings and such into bad places, like between IC leads. When power is applied the shorts can weld or solder themselves in place and be resistant to being dislodged by compressed air, vacuum, or shaking. On the underside there are lots of metal stubs that can get bent over, possibly shorting to the ground grid artwork that surrounds a lot of them.
Also, take a close look at the sheetmetal deck and card guide metal for metal whiskering, a kind of velvet fuzz growing out of the metal surface consisting of pure metal whiskers that can break off, drop onto the MB below and short out stuff. I had one SE/30 chassis that was growing this stuff. I cleaned it off with steel wool but never really trusted it again and eventually it became a parts unit.
If you decide to blow or vacuum the PC board be aware that the nozzle can develop a static charge from the airstream friction. If you hold the board ground and the nozzle near the tip with your two hands the static will pass harmlessly thru you rather than jumping from the tip to burn out the components.