Newbie in need of some direction. I just got back a 239 flathead that I had rebuilt and need some assistance installing the distributor. Do I just align the timing pointer to the timing mark on the pulley and install the distributor with the rotor pointing at #1 on the distributor cap.

 

Yep, same as for any other engine (pretty much), but you have a 50-50 chance that without further checking, you are at TDC on the exhaust stroke. If you have the #1 plug out, you can crank it over with your thumb over the plug hole; when it blows your thumb off the hole, that's compression stroke TDC. You'll likely have to back it up a ways to get the marks aligned. By the way, the marks are actually at 3 deg BTDC, which is where the timing gets set at idle with the vacuum line disconnected.