The bigger a part is, the more heat you need to apply to get the solder to flow out properly. The two big resistors on your C4S boards in the R2 positions need more heat for the solder to flow out properly, and the MJE5731A transistors also need a lot more heat. You can set your iron on one of these solder joints, add a little bit of solder, then count to 5, then pull it off. You'll also see the solder suck into the board at some point when it has gotten hot enough, and you want to leave the iron on just a little longer after that happens.