Don't delete any log files that show up in your Exchsvr\MDBDATA directory. You are probably getting a lot of 5mb files created, sometimes a new one every 5 or ten minutes. The way to keep the number of log files down is to do a full Exchange Store backup regularly. When you do the backup, the logs get flushed into the database, and all data is "committed." When you delete these logs, you run a great risk of corruption or not being able to recover your data in the event of a failure.
To do a proper backup, you can use NTBackup or BackUp-Exec or any other Exchange-aware backup program. I back up my Exchange Information Store every night, and I don't have trouble with logs. If my backup server goes down and I run for a week without a backup, I get in the same sort of trouble that you are in.
Some might tell you that you need to enable circular logging, which limits the number of log files that get created to a certain number, but this can bite you when you try and restore from backup and find that you can't restore any data since your last backup. Having the log files on hand (in a number limited by a recent flush via backup) is the best way to be able to recover right up to the point at which the information store got corrupt.
ShackDaddy