What I have: I have a large data-set containing links (bus routes( (>2000) and their respective nodes(bus-stops) (>6000). The data set I received from the local bus operator is very messy. It contains multiple variations of names and multiple (nearby) locations for the same stop. There is no clear trend of these variations, so I cannot run a program (say, to merge all points within 50 m radius etc. Example in orange and yellow circle in the picture).
What I want to do: I want to use QGIS clean the data manually.
Is there a method/plugin that lets you select multiple stops and merge their locations either to one of their locations, or even a manually entered location?
I now have ArcGIS (10.2) also, so a solution in either QGIS or ArcGIS is fine. Here is the screenshot from ArcGIS.

The points highlighted in yellow the circle are actual locations of the bus-stops. I want to merge them into one data-point(consider it as a node), while retaining their attributes. (attributes contain information about which routes pass through the stop and what order is the bus stop in a particular route etc ).
So if these data points are like this:
- "Intersection xyz1 (Besides Public School)", lat1, long1, route 23, direction up
- "Intersection xyz2 (Besides Govt. Hospital)", lat2, long2, route 23, direction down
- "Intersection xyz3 (Besides General Pharmacy)", lat3, long3, route 87, direction up
- "Intersection xyz4 (Besides Open Area)", lat4, long4, route 87, direction down
They should be converted to:
- "Intersection xyz", lat, long, route 23, direction up
- "Intersection xyz", lat, long, route 23, direction down
- "Intersection xyz", lat, long, route 87, direction up
- "Intersection xyz", lat, long, route 87, direction down