The Mechanics solder paste is not great. But I use it successfully.
I use IPA to clean my boards and have only rarely had resistant patches of baked flux that need scraping and then further cleaning with IPA.
I brush on IPA with a very wet toothbrush... let it sit for 30-60 sec and then wipe it with a lint free cloth.
I repeat this process several times but lay the cloth over the PCB and use a dry toothbrush to soak up the resin and IPA.
I notice a couple of issues on those boards that might help.
1. As someone else mentioned, you are not getting good flow over the whole pad. In addition, to the flux issue, you may also encounter problems with tombstone caps etc.
2. It appears that generally you have way too much paste on the pads. The problems with this are exacerbated by #1.
To improve this process, I think you need to look at your reflow cycle.... You are not allowing enough time for the solder paste flux to do its job.
You also may be too hot and too long in the solder phase. Mechanics paste has a fairly low melting point and that flux tends to bake on if it hasn't evaporated. I usually limit my peak temperature to about 200°C. (measured on the PCB)
For #1, you need to make sure that your PCB is perfectly clean. Then, with home brew boards I usually flux the entire board with a flux pen before applying the solder paste.
For #2, you need to reduce the amount of solder paste. Remember, the more paste, the more flux but of more concern is that some of the extra solder may end up floating the passives high and then shorting underneath them.
Graham
I see you just posted an response.
Some of your problems are aggravated by the things you suggest we ignore, but some of the above suggestions should still help.