I always assume that no external libraries are used unless stated.
In this case it is certainly not necessary to change the REFS field, you can mix all inputs between input/analog or outputs without any problems.
I don't know about AVRs, I don't use them and don't use external libraries, I'm an original LDmicro user ;)
The use of Timer0/1/2 is only important with PWM.
if you make a mistake ldmicro will give an error.
Configword: 2F42 and 3F72 will both work well with the Pickit2/3, I always use 3F72.
For the newbies among us, LDmicro works perfectly as it exists now, don't look too far, usually it's a selfmade hardware failure if the ldmicro simulation works well.