I'm having trouble converting this .mkv file to .mp4

Use Handbrake. handbrake.fr/

plop the file into handbrake then hit convert, I would recommend though multiple tweaks to the default settings

1. Switch "Peak Framerate" to "Constant Framerate" under the Video tab.
2. if it is a PAL or Film recording switch it to 25 or 24fps in the settings. you can check what framerate your file is by right clicking on the original, then hitting properties, then details.
3. Change the quality settings from "Constant Quality" to "Bitrate"
4. Change the bitrate to higher than default. Using the same procedure you used to find your original files framerate, you can find its Bitrate. You can put the bitrate lower, which will make it lower quality. But make it use less space.
5. CHANGE THE DEFAULT AUDIO COMPRESSION. Handbrake has it automatically on AAC 160kbps. This sounds pretty bad. I would recommend putting it on "Auto Passthru" which will put the original audio track into the new file. Do note that most DVD audio [AC3] will not work in some video editing software such as Vegas. If you are doing this for video editing purposes. Set the bitrate to AAC 320kbps.
6. To speed up encode time under Filters switch De-Interlace to off. However if it is a DVD or VHS source. Switch it to Yadif.