"2 device PCIe cable"--oops, I meant IDE. I can mail you one of those if you need extras. But I don't think any of mine get you past the issue of two of the connectors being close together. Have you tried moving the DVD drive down?
$100-$150 to "fix" this might not be worth it. I could mention alternatives "HEY I LOVE TO BEAT MYSELF UP AFTER THE FACT educate me please,WTF", but what's done is done and you got a decent enough price for what you spent. The fact that your motherboard supports PCI-e and DDR2 makes it substantially better than I thought it was.
Considering it can run DDR2, you should. It's better. I'd mail you two 1GB sticks of DDR2 for free.
This is your motherboard, right?
http://www.newegg.com/Product/Product.aspx?Item=N82E16813157115
Btw, do you have the Pentium Dual-Core E6700 or the Core 2 Duo E6700? The Pentium one is faster.
Down the line you can upgrade this motherboard to 4GB DDR2 (2x2GB) and a G0 stepping (95W) Q6600 or similar 1066MT/s fsb Core 2 Quad. And perhaps a more important upgrade...is your GPU the DDR2 version of the 4650? If so, then you could see a HUGE!!! graphics improvement if you upgrade to something like an 8800GT for $20 or so:
http://www.tomshardware.com/reviews/fastest-graphics-card-radeon-geforce,3085-7.html
Just make sure your PSU can handle whatever you get (I'd suggest a Corsair CX430 for the PSU when the time comes).