> to set the dimensions of the project
jspaint.app (which I used) actually has resize dialog under Image > Attributes (and if I remember correctly this is same as in old Win98 Paint)
> I made my palette outside of paint
the trick was to actually make palette/template image and then use picker to pick these colors
> layers...
this is biggest difference between old paint and new modern editors. There are some tricks how to emulate layers using copypasting and multiple instances of paint, but I actually forgot how this was done back in the days. We probably don't cared about this as we were just kids playing with computer.
I actually like painting in mspaint, probably because I was used to in past.