OK I did find one outstanding issue with mastercoin-explorer - it still counts the same address multiple times in one purchase. For instance, on this transaction:
http://blockchain.info/tx/52a875a46d7973760974b2ae8fa7bb71bfe7d06e0be8fd2bf2e20eaca182dbd7When I enter the purchasing address (196V2uB471HoMHwbkQRQRiwd3aYpU6RtWg), I get "Bought 210000.0 Mastercoins and got a 88206.42361111111 Mastercoins extra."
The buyer sent 420 BTC with 5 inputs of 100 BTC each and 80 BTC change, which should have been 42000 MasterCoins plus a bonus. 42000*5 = 210000 which implies each input is being counted.
Probably related is the bug in the handling of this purchase:
http://blockchain.info/tx/37992e445c33dd74a1e4e00dabb6a66f16a5d39977a1f5fd1a6c0154e884eee215XJoDF4xCUrWX3ES9ftWq3wnGhuRsqrLk (which had the largest total input) should be the owner of those MasterCoins rather than 1G6F8aMJNp3zMG9L1DxDT3WjiUntJYwYka (which had the largest single input). MasterCoin-Explorer incorrectly credits the latter address with the purchase. I realize I need to be more clear in the spec about how to do this!
Also, a quibble: MasterCoins are only divisible to 8 decimal places, so calculated bonuses should be rounded off at that precision

Thanks!