1)
Is this the same 1000 Amos?
1.
Rashi: No. It is another 1000 Amos. The water became deeper.
2)
What is "Mayim Birkayim"?
1.
Rashi: The water was until his knees. Radak ? even though Mayim is Samuch, it has the suffix Mem (for plural), like "Amarim Emes" (Mishlei 22:21), "Sigim Kesef" (above, 22:18) and similar verses.
3)
What is "Mei Masnayim"?
1.
Rashi: The water was until his loins.