Nub, thought/comment regarding your video card and clearance on the CPU heatsink shroud. I have an XPS 410 here with a double width video card in it like your card. This machine has a 9800 GTX so the comparisson should be very close (since I have not seen yours in person).
From what I see on my machine here the CPU shroud does not make contact and less than half of the GPU induction fan is 'shadowed'. I say shadowed because it is not in contact and thus not really obstructed. Now, I know you have stated you had to modify your card to fit so remember I am not disputing that... just sharing what I find in this comparisson. the machine I have here may be slightly newer/different.
If this closely compares to what you are seeing in your case, in that the GPU induction fan is not blocked, I would not worry at all and put the side back on to your case. The E6400 CPU runs relatively cool and your internal temps should be very well within any reasonable limits. If you have any worries about specific temps in yoru machine download a program (free) called CoreTEMP at
http://www.alcpu.com/CoreTemp/. I use this app frequently.
Also, in closing, I would mention that you should be aware that many computer cases are designed around air flow. Leaving the side off your case is (in many situations) actually worse for cooling becuase impact areas for forced airflow are disrupted. Just thought I would throw that in there. Some machines (The Dell Poweredge sc1430 for example) will not run if the side panel is detected to be missing.
I am happy to offer feedback in more detail if you want to PM me a pic of your video card installation. I have tried to replicate it here but I am not sure I have an accurate copy of what you have.