However its throughput was low (3A max) so to get more I am now going to be using an N channel MOSFET.
I don't think the throughput was limited because you had P-channel MOSFET. A good old IRF4905 has 0.02Ohm resistance when it's on and it's not spectacular in anyway. Sure an N-channel gives you even better, but something else was the limiting factor.
As a result I have the problem now of having a common positive instead, and that is where my problem lies. I can measure only the one side otherwise I cause a bypass of the MOSFET by tying the negatives together.
I'm not 100% sure I understood your problem right, but see attached picture.. If you're measuring the panel voltage with an ADC it's easiest to do a voltage divider between the common positive and the negative of the solar panel. ADC sees a decreasing voltage when panel voltage increases, but the code to convert it back is just one line.
I'm wrecking my head trying to think of a way around this and so far I've got myself nowhere. I was hoping someone here has had this issue before and could advise on an approach?
Don't worry.. you'll figure it out. It took me some time

to get this stuff right. It gets messier when you want to get rid of the blocking diode.
I've made couple of revisions of my own solar charger controller. Learning power electronics things was part of the motivation, but another reason was that the commercial charge controllers have relatively high quiescent current, that became a real issue, because during December there basically is no sunlight at all here and very little in November and January (the installation is located 64 deg North). That combined with the fact that batteries perform poorly in low temperatures I got much better results with my own design, that wastes only 100µA during darkness. The best commercial option I've found for this unusual requirement was around 10mA (factor of 100 difference!). In my application the average load is 1-2mA with 2A peaks when it activates (very rarely). One solution would have been a very big battery but it was physically impossible in my application.