Greetings and salutations, Dan,
I've had situations where my connected mouse and keyboard seems to take on a life of their own and applications that don't seem to seem to see either. Good job in locating a work-around for this, but let's get it working like it's supposed to.
If you've tried any of the steps I'm about to suggest, feel free to skip them. Test the Mail app and trackpad after each step.
Reset the System Management Controller (SMC) on your Mac
How to Reset NVRAM on your Mac
Try safe mode if your Mac doesn‘t finish starting up
How to test an issue in another user account on your Mac
OS X: About OS X Recovery
If you're still having a problem with the trackpad working in the Mail App, I recommend reinstalling OS X El Capitan. Even though reinstalling the operating system shouldn't touch the personal data on your MacBook Pro, for safety's sake, I always recommend having a back up.
Use Time Machine to back up or restore your Mac
Here's the instructions for reinstalling the operating system
How to reinstall OS X on your Mac
If those steps haven't corrected the problem, you'll need to have an Apple Store or Apple Authorized Service Provider evaluate your MacBook Pro. You can use the following link to locate the nearest one
Find Locations
If you're unable to locate one close enough, you can contact Apple Support for all of your service options using the following link.
Get Support
I applaud your patience with this problem, and I do hope you have a great day!
