As requested here's the packed data and a test bench you can test your own merging function ideas and replicate my results (hopefully). If you want the plots you can use the end part of scripts in part1 part2.
The data is a bunch of super secret Eve Online killmails. The first part of the script handles the json to data.frame transformation. After that I introduce the R core merging in a for-loop, data.table variant, reduce function variants, and finally the fast.merging. There's actually alot more data then we are using in the bench. Totalling 166106 killmails, merging only 3000 of those. That is because as noted in previous posts the merge for-looping seems to work in exponential time so going much higher then 3000 lines seems really excessive. Even now it took over an hour to run the whole bench on intel i5 3570k (not overclocked). So if you want faster results choose 1000ish frames and set rbenchmark replications to 1. With low frame count (under 100) the results are fairly similiar.
If you are going to test are the results from different functions the same, note that the order of rows and columns will be different. I'm eagerly waiting for you results and ideas.