For someone new to board layout, four layers definitely is a challenge.
So, first of all I'd like to strongly recommend looking into making your board more modular. You surley don't need all these voltages at the same place, so routing them only to the parts of the board where they are needed is strongly recommendable. From your question's tags, I'd presume you can have one or two voltages that you distribute across the board and have the voltage regulators that generate the locally needed voltages right where they're needed – that should solve a lot of the complexity issues.
"Data acquisition" doesn't even necessarily sound like you'd need a power plane layer; it's often a good idea to have a ground plane layer, but unless your data acquisition happens at millions of samples per second, with low pass filters (you'll need those, anyway! Never use an ADC without an appropriate filter – you'll get a lot of aliasing!) closely locateed before your digitizers' inputs, you should usually get away with simply making sure you have a continuous ground plane below your most sensitive signal lines, where you especially avoid fastly switching signals.
Other than that, PCB design is both a thing of experience (so go ahead and layout your PCB, look at the result, throw it away, do it again with all that you've learned), and of schooling – you might want to get a good book on that. Books are cheaper than broken PCB manufacturing, and much less frustrating. Believe me.
Another word of advice: Don't reinvent the wheel. You don't say what your application is, but chances are, someone before you has done something similar enough for you to buy or learn from that.