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Well this might not help , but when I was doing place and route for Altera 600k parts and was getting to about 75% utilization the P&R slowed down alot. Exponential as utilization increased. Took me about 2.5hrs. I then upped my memory from 1gig to 4 gig and the performance increased about 25%. This is because the P&R tool did not swap to the hard drive. The biggest thing was I went to the 1500 ( 1.5 million part ) . Expensive but saved time!!!!. The utilization went to 15% and the time for route was a little over 30 min. So I would tell you for prtotyping use the biggest part.
You do not have any chance if you want to achieve a good performance. I have tried many times, on a very powerful system with 4 Giga RAM. Especially for big Stratix devices is quite normal to spend around 8 hours for a design.
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