New motherboard don't support AGP, and getting one that does will limit you a lot.
PCI-E is the future, and as for an aftermarket cooler, if you want your system running cool, and with headroom to overclock, its best to get one.
The Freezer 7 is good, the Zalman 9700 is probably better (and quieter too), especially for the Core 2 your getting now.
If you could afford it (not much more), the Tuniq tower would do amazingly well, but thats only if your going to overclock loads.
You'll be happy with the Zalman 9700, I am, and I'm a perfectionist..
But yeah, don't bother with the AGP card. Its not worth it. Especially for 2 months. Sell it if you can
The X1950 is a really good card for current Direct X 9 games, but it isn't future proofed, but...what hardware is these days? It'll be fine, and its cheap