Hi, I had a problem with a big project similar to yours. I had approx 600 source clips and before they could all be imported Prem crapped itself.
What I did was use VirtualDub to join the source clips together using a ‘direct stream copy’ which doesn’t recompress – so no loss of quality. I did this for different categories of clips, so I would join the clips together in groups of approx 50. That way, when I imported into Prem, I only had 12 source clips! Then you bring those clips into the timeline and cut them back up. A pain, I know, but a way around your problem.
Good luck!