When I was running the engine on the stand, I used the default tables and only modified a handful of settings specifically to the engine. It started and ran "fine" that way. Once I moved everything into the vehicle and was ready to actually start tuning, I wanted to establish a more rational baseline to work from. The very first thing I did was upgrade my MegaSquirt firmware to the latest version. Mine was very old (3.1.0 vs. 3.4.2), and this change alone made the engine run noticeably better. I then made changes to the settings and tables following the approach of Andy Whittle on YouTube. Lastly, and this made the greatest improvement, I generated a new initial ignition table.
You can watch Andy's initial setup how-to video here. In just 11 minutes he walks you through the key initial settings that are specific to your engine and sensors. Since I am not running boost, his instructions on how to change the scales of the MS tables to give greater resolution for N/A builds was a nice insight. If you've done a MegaSquirt build before, there is really nothing new here, but for us first-timers, it's a concise, helpful walk-through.
For an initial ignition table, this tool is really handy. The table it generated with M10 specific information was radically different from the default table and dramatically improved running and driving. In the image below you can see the data for the M10 typed into the tool. Your idle vacuum may vary. If you don't have a vacuum gauge, you can calculated the idle vacuum from the MS MAP reading like this: Your in-Hg of vacuum at idle = 0.346 * (100 - your kpa of MAP at idle).
I made one more change after driving around for a bit, which was to turn Overrun Fuel Cut-off on with a delay of 0.5 seconds. This eliminated deceleration backfiring, which was really intense since I was driving with no exhaust system.
I hope this has been helpful.