Are you still using v9 as your profile indicates, or have you now upgraded to v10?
You may find that you get better performance if you can load your Excel tables into an Access database, and then load the Access table into Monarch instead of from the Excel file. It might be a bit of an up-front task to convert your Excel files initially, but it might be a worthwhile exercise.
I assume that if this is advantageous, you'll likely need to look at the processes that create the inital Excel files too, if you're the one creating them in the first place, that is. This could be a bit of an undertaking if you have a lot of them.
If the Access approach is cumbersome, then try exporting the Excel files as CSV files. Try a converting a couple of the larger files to Access and/or CSV as a performance test. Do they load any faster into Monarch?
If you're supplied the Excel files by another party though, this might need some thought.
Using v9, I read in an XL2003 file with about 60k rows and 23 fields, a mix of character and numeric data. The load took about 9 seconds to immediately go to the bottom of the table upon being presented with the Table window.
I then exported that to an XL2007 file, and opened that as a database in a new Monarch session. Jumping to the end took about 25 seconds, and there was a significant pause when using the wizard.
So is the Access approach a usable long term solution for you for your larger data sets?