It's completely up to you, honestly. For sure the graphics card is what's blowing you on the flash performance, I promise. If you go for the 4,1 or 5,1 route, I would get a dual socket computer, because they will be the most upgradable. Get an 8 core 4,1 and then when the time comes, flash it to a 5,1 and upgrade the processors to 12 core if you ever need it. That being said, I personally believe the 3,1 will do what you need it to with a couple more upgrades, but it depends on how long you want to keep it. I plan on keeping my 3,1 for at LEAST another 3+ years, but I have it upgraded basically to the max. It's for sure your call, but it depends on how much money you want to spend, and how long you want the computer to last.
I would give the 3,1s about 3-5 years before you'll need to get a new computer. However, in 3-5 years, the 3,1s won't be worth nearly as much as they are now, but hardware advances are still coming.
I would give the 4,1/5,1 a minimum of 5 year lifespan from now, since they are basically the same machine. Especially the dual socket computers, they will go from 8-12 cores with upgrades down the line.
nMP is obviously the new machine at the moment. I know many people that are very happy with their nMP, and many that are dissatisfied and want more features. However, 3+ years from now, the future Mac Pros might be exactly what you're looking for.
Hope I could provide a bit of guidance, good luck in whichever route you take. Always glad to help.
-N