I've found the .points file
these are my waypoints:
name:Hometown,x:196,z:128,y:67,enabled:false,red:0.0,green:1.0,blue:0.0,suffix:,world:,dimensions:-1#0#
name:Oil derick 1,x:319,z:260,y:68,enabled:false,red:0.08200657,green:0.49727243,blue:0.48210442,suffix:,world:,dimensions:-1#0#
name:Lower Mine exit,x:164,z:171,y:23,enabled:false,red:0.8887612,green:0.03684789,blue:0.49940395,suffix:,world:,dimensions:-1#0#
name:Upper mine exit,x:150,z:166,y:28,enabled:false,red:0.19834173,green:0.0077989697,blue:0.47189015,suffix:,world:,dimensions:-1#0#
name:Village 2,x:-400,z:562,y:80,enabled:false,red:0.68413204,green:0.7771675,blue:0.9281636,suffix:,world:,dimensions:-1#0#
name:Cracked sand dunes,x:84,z:-165,y:63,enabled:false,red:0.39139342,green:0.6845915,blue:0.796281,suffix:,world:,dimensions:-1#0#
name:Nether Portal,x:256,z:136,y:72,enabled:true,red:0.8041143,green:0.3479002,blue:0.32849854,suffix:,world:,dimensions:-1#0#
name:hole1,x:324,z:152,y:81,enabled:false,red:0.81671184,green:0.61092114,blue:0.5362261,suffix:,world:,dimensions:-1#0#
name:Hole 2,x:208,z:192,y:64,enabled:false,red:0.31222087,green:0.5994141,blue:0.70723176,suffix:,world:,dimensions:-1#0#
name:diamond 3,x:221,z:197,y:11,enabled:false,red:0.52213377,green:0.18548965,blue:0.1446721,suffix:,world:,dimensions:-1#0#
name:Mine 2,x:437,z:212,y:46,enabled:false,red:0.75722396,green:0.77093923,blue:0.6143347,suffix:,world:,dimensions:-1#0#
name:Double spidey spawner,x:452,z:246,y:42,enabled:false,red:0.3424031,green:0.22780794,blue:0.80260706,suffix:,world:,dimensions:-1#0#
name:nether Fortress,x:-2904,z:520,y:68,enabled:true,red:0.9437701,green:0.13842702,blue:0.30423588,suffix:,world:,dimensions:-1#0#
name:Hole 3,x:214,z:52,y:16,enabled:false,red:0.48505092,green:0.93164307,blue:0.5647037,suffix:,world:,dimensions:-1#0#
name:Spider spawner,x:206,z:75,y:20,enabled:false,red:0.17811292,green:0.61927146,blue:0.44704503,suffix:,world:,dimensions:-1#0#
...they have both -1 and 0 at the dimensions bit
what exactly should I change them to?
The two in the nether are these:
name:nether Fortress,x:-2904,z:520,y:68,enabled:true,red:0.9437701,green:0.13842702,blue:0.30423588,suffix:,world:,dimensions:-1#0#
name:Nether Portal,x:256,z:136,y:72,enabled:true,red:0.8041143,green:0.3479002,blue:0.32849854,suffix:,world:,dimensions:-1#0#