1: start with a view matrix all 0 except for [2]=-1, [4]=-1, [9]=1, [15]=1 instead of the regular identity matrix. that should correct your view matrix for quake's coord system
2: the problem is unlikely to be your perspective matrix. any weird/missing polys are more likely due to the y rotation of the view not being handled by the frustum code, resulting in culling - the culling is likely as correct as it was for regular glquake, fix the view matrix instead/first.