For large projects, always make sure you have an SSD drive in your pc/laptop.
Also, don't use the build in DB but something like postgres.
To clean up the jar files, make a new empty project in the Mendix version you are currently using. Then import all the Modules you use in your current app from the app store.
Backup your old folder containing all the jar files and empty the folder. Then copy all the jar files from your new project.
If something is missing you can always grap a jar from your backup.
Mx7 is just much slower then Mx6 IMHO. We moved from Mx6 to Mx7 a couple of weeks ago and noticed that running the app took twice as much time as before. We are now in the 15 minutes range before the model has started. And for some reason I feel that doing restarts are also less efficient (ie doing a complete proces instead of just updating what has changed). Overall productivity has decreased at our office due to the upgrade.
Are you using the built-in-database with lots of data?