You have a lot of good questions. I'll try to answer of few of them. I'm not an expert but I can pass on what i think I've learned. I give no guarantee of the accuracy of my answers.
It sounds like you have a good setup. I have found my MTR3b to be a great performing little radio and I have found QRP in general to be very effective. I've also used end fed antennas almost exclusively with QRP and they have worked well for me. That being said, QRP is a lot like fishing, if you don't stack the odds in your favor you may get a bite and you may not. Calling in the blind is the least optimum way of securing a QSO. Some days you snag a good one and some days you get nothing. When you are testing out a new antenna or radio it can be disheartening when your first trip out returns only minos. You have a great SOTA setup. If you self spot a SOTA or POTA activation you will stack the odds in your favor by bringing the fish to you. Now you are being chased by others who would have not know you were there or wouldn't have been interested in a contact with you otherwise. I have gone out on consecutive trips outdoors with my MTR and not had one bite. I started to wonder if my setup works. Then I go activate a summit (spotting myself) and in 20 minutes make 30 contacts nationwide using the same setup.
To address some of your questions specifically:
Half wave wire antennas when in free space (or when more than half a wavelength above the ground) radiate mostly broadside. They also radiate off the ends of the wire but not as much. As the wire is lowered below half wavelength to the ground the horizontal radiation pattern turn more and more omnidirectional. A 40 meter half wave antenna only 20 feet off the ground will have a mostly omnidirectional radiation pattern. As for the takeoff angle, it will be quite high and NVIS will work if NVIS conditions exist for 40 meters at the time and location of your activation. Ground losses will not be too high for NVIS if NVIS is available. I have used NVIS very effectively with 3 watts. Your takeoff angle will be high, as I said earlier, but it will be low enough for a communication range of a few hundred miles in average conditions. I have found midday 40 meters to usually work well between 300 and 600 miles with my end fed antennas and QRP CW.