Resets
When MegaSquirt® resets, MegaTune displays a 'RESET X' in the lower right corner (where X is the cumulative number of resets (including restarts)) - it will also beep. Resets can cause a number of problems that cause the engine to run badly, including messing up the baro correction and enabling after start enrichment. So you should try to cure any reset issues before putting a lot of effort into tuning.
Resets generally indicate that the power to the processor was interrupted. This could mean that the input power actually was cut, but it can also mean that there was a power surge into the back plane (ground), so that there was no longer a 5v differential between the inputs and the grounds...
Resets are often caused by noisy power supplies (usually the alternator), or poor grounds.
First, fix the grounds, make sure all are perfect and do not connect to areas that are dirty, rusted or painted. Place them close together.
To check the alternator, you can shut the engine off, remove the wiring to the alternator (don't let it ground on anything, some wires might be hot). The start the engine and see if the resets go away. If the resets disappear, the alternator is the problem.
You can fix the alternator and/or add a car stereo power filter to the MegaSquirt® controller's 12V supply. These are cheap (~$5) and widely available. They typically have three wires: one from a switched 12V source (the original source for the MegaSquirt® controller), one to go to the MegaSquirt® controller (with clean power), and a ground wire. Ignition noise, solenoids turning on or off, and that sort of thing can also cause resets. Check your harness routing to see if any ground or signal wires are near noise sources such as spark plug wires or the coil. Finally, non-resistor spark plugs have been known to cause resets. Use resistor plugs whenever possible.