Your question isn't entirely easy to answer. You're missing a few pieces. Like, were you creating clustered indexes in the first sequence, or non-clustered indexes? Secondly, did you change any of the other Select queries like you did the first one?

Things like that will change performance. None of us can give you a decent answer to your problem with the pseudo-code you've listed. However... I can tell you this. Clustered indexes suck for data insertion. They're great for reads, not so much for writes. And 50 million rows? That's a LOT of data. I'm betting your second attempt spent most of that 4 hours just on part a.