As far as marathon goes, I think that 100k is a good number. Like mingee said, 100k was the max score in the predecessor game tetris attack, so it feels natural for that score cap to carry over. I also like 100k over 50k because I think this category should be longer than the regular time trial mode. It's very easy to get 50k under a minute. 999,999 seems way to big of a score. Even for a highly skilled player it's going to take 30~ minutes. If adding this category is to bring in more people to the community that would be very off putting. Newer players would take hours to get that score which would probably discourage them from playing more.

As far as difficulty I think that shouldn't matter at all. In the past when score was the main focus of puzzle league (like early 2000s), the difficulty was never considered and categories were only split by mode. 1P time trial, 2P time trial and endless were all considered different categories. If you played 1P time trial on easy normal or hard they were all compared to each other. Play on whatever difficulty you think you can get the best score with. I feel like that should be kept as well.

In the past though, marathon for pokemon puzzle league wasn't really considered and we only did it in tetris attack, so a standard for ppl wasn't set then. My vote goes for 100k with no distinction between difficulties.