Hi BitShard,
Do not make biginners mistake's en put al your energy in designing the digital part! ;-)
1e
Design the analog part, make sure its works OK, test it dynamic, you need a scoop, pulsgenerator enz.
2e
DC-DC converters are difficult and they push high frequenties in your analog circuits, it is difficult to screen them.
3e
A low noise PSU with DC-DC converters(high power), is extreemly difficult.
4e
NO, CPU in the voltage or controle loop!
5e
Use "real" opamps, not lm324
Take a look at ADA4077 series.
6e
Make shure that you know what "Phase Margin" is, extreemly important to keep your design stable.
If you insert an current sense IC, you make the phase margin worse, thats normal, but keep in mind when designing of the analog part.
If you ignore it, the circuit will certainly generate when the current limit kicks in.
Just 2 cent...
Kind regarts,
Blackdog