As a scientist, mathematician, and engineer, I think I understand fairly well what scatter plots do well and where they fall short. I don't yet understand why one of Excel's built in scatter plots won't work:

1) This should be the default behavior for a scatter plot. Choice of dot or dash or square or triangle or whatever are fairly easily controlled using the format series dialog.
2) As long as data does not change in the spreadsheet, they should not change in the chart. If you assign the X and Y values ranges appropriately, it should be easy to add as much data as you want to the chart (up to Excel's limitation which are quite large for 2010). When you are ready to clear the chart, simply clear the data range and start filling with new data.
3) The easiest way to "tag" a data point with a value/text from a range is to use Rob Bovey's XY chart labeler add-in, or to use 2013 or later, which has this functionality built into Excel.
Also we are looking at maybe having the item be colored a special color if both (axis's values are NEGITIVE) EXAMPLE x=-1, y=-5)
The easiest way I have found to "conditionally format" data points in a chart is to plot each "color" you want as a separate series http://peltiertech.com/conditional-f...-excel-charts/

I personally tend not to use the chart to calculate distances or rates, preferring instead to calculate those kinds of quantities in the spreadsheet. I can use a chart to visualize things and help see how to calculate any derived quantities I want to calculate, but I don't find the charts themselves very useful for computing quantities. Perhaps this is why you don't want to use the built in scatter plots, though I don't see how the spreadsheet you have is going to help with these (possibly because I do not yet understand everything about the project you are undertaking.

I don't have immediate access to Excel right now, but, perhaps if you walk through the analysis once, I can better understand what you are doing and can make better suggestions.