For cuttingg off, i think the biggest danger lies in accidentally connecting the several layers of the PCB while sawing. so maybe just double check the cutting edge afterwards with a maggnifier and if needed sand it off a littlebit? i think most everybody is fine, maybe yu just had really bad luck last time. iirc people reported using a proxon/dremel w very good results.
for DC input afterwards, you would either need to set up your own DC/DC circuit to get from 9v to the axoloti 3.3/5v, or, recommended, you reuse the cut off midi part for its poweer converter and reconnect the 5x pin header at the cutting edge. if you need the space you can consider unsoldering the midi din jacks from the cut off part. but that part also contains the voltage converters/regulators etc.