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I have some data that should be spatially joined, but from small precision differences (less than 1 in) they aren't joined. I've found no way to add tolerance to qgis spatial join operation. Is there a way to config a tolerance value, or a plugin to correct small distances?

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I would save the data layers into PostGIS or Spatialite and use ST_SnapToGrid http://postgis.net/docs/manual-2.1/ST_SnapToGrid.html. You can either update the geometries and make a permanent fix or then you can use ST_SnapToGrid on-the-fly in SELECT statement if you do not want to change the original data.

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I believe that this question has been asked previously, Joining attributes from nearest point in QGIS? if that doesn't suit then perhaps buffer the joining features by a small distance (a few inches should do) and then join to that.

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