Does the ej22 phase 2 do a direct swap into a 99 Legacy?

Legacy L's already have them. If it's a GT or Outback, then no, the replacement is a Phase I. Also the Phase II EJ222 is not the excellent engine the Phase I was. They have a tendency toward oil consumption and rings are dealer only and very expensive. You may as well just use a Phase II 2.5 as they were essentially the same with 20 more HP.

GD

Yes 99 legacy's are Phase II.  As GD said they're not robust machines the Phase I EJ22's were so don't wasn't time or pay top dollar trying to find one - just get an EJ25, there's more to pick from.