The Dayton sub is powered so no concerns there. The Yamaha should have no issues if you go with some efficient speakers. For your front three, there are a number of options within your budget. I've listed a some of them below.
Ascend Acoustics CBM-170SE FL/FR and CMT-340SE center: $650
Cambridge S30 (3x): $400 (I'm not sure you can purchase singles)
Infinity Primus 163 (3x): $330 (Amazon)
HTD Level 2 or 3 (2 pair): $400/$600 (HTD may sell singles, not sure)
Arx A1b (3x): $450
Wavecrest Audio HVL-1 (3x): $335
Ascend Acoustics CBM-170SE FL/FR and CMT-340SE center: $650
Cambridge S30 (3x): $400 (I'm not sure you can purchase singles)
Infinity Primus 163 (3x): $330 (Amazon)
HTD Level 2 or 3 (2 pair): $400/$600 (HTD may sell singles, not sure)
Arx A1b (3x): $450
Wavecrest Audio HVL-1 (3x): $335