I had similar problems 5+ years ago with an exported GTFS feed. Some of the issues:
1) Duplicate stop IDs, 0 feet from each other. This required work in the source dataset, or filter and removal in the export.
2) Estimated stop times for non-scheduled stops from the source data set. These were to-the-minute estimates, and FeedValidator uses to-the-second estimates. The solution was to omit the estimated stop times and only include the scheduled stop times in the GTFS feed. Google fills in the blanks from its own mapping algorithms.
3) Actual bad route information in the source feed, such as a bad start time for a route leading to a fast cross-town time. Need to be fixed in source.
In all cases, it was issues in the source feed and our custom GTFS exporter, and no tools helped. Also, warnings in FeedValidator became errors when we submitted to Google, so it is worth eliminating them.
- John