it depends.

if you mean for the whole car end to end, I am not sure if it is worth it.
expense wise, there are plenty of kits out there that you can modify to your hearts desire that are cheaper than you can build it yourself.

if you mean something like an engine harness or tail light harness, then sure. I wouldn't bother to use factory ends unless I need them, and then I would just take apart the original and make new ends using those connectors. for the rest I would use weather pac connectors.

I rebuilt my own tail light harness doing that and using new tail light ends.
BUT I only had to deal with 4 colors of wires.

An under dash harness is probably 15 or so colors with and without tracers.
Can be done, and honestly could be simplified quite a bit with a few relay's etc.. but would be expensive due to the sheer number of spools of wire required.

the common ends are available at napa, but you have to take appart the plastic part of the connectors to reuse them.
some simple tools allow you to do it pretty easy.

If it were a completly custom car, then you really don't have a choice but to wire your own. But you would be better off not to limit yourself to the stock connectors unless you have to plug into something factory as chrysler is a pain about allowing someone to make the correct connectors.
that is why most aftermarket universal wiring harnesses use GM stuff.