What does Bonus Points Remaining mean in league play

No, your challenges and intel will not reset. From what I have observed changing the difficulty does not affect intel either. In otherwords, if you're having trouble getting at it, play it in the lower difficulty.

One quick note however. If you are replaying missions in attempt to gain some of the "missable" achievements (ie. You must make specific decisions across various successive missions etc) then you must use the "Continue Story" option rather than "Mission Select" when progressing past the starting point of your rewind.

All of these questions can be answered in the wiki, but here goes:

The order in which you hit the towers changes each game. To determine the order of which tower to hit with the galvaknuckles (from the wiki):

There are Mahjong tiles of different colors and sizes located throughout the map. These tiles essentially hint in which order the player should melee the radio tower with the Galvaknuckles (see step 8). There are eight tiles, four with Chinese symbols and four with a different amount of dots. The Chinese symbols reflect "east", "south", "north" and "west", and the dots tell the order each side is hit. Each compass point and dot tile is colored, and same colored are correlated. For example, if the player finds a green 'north' and green three dots, the north side of the tower is hit third. This order changes every match. If you make a mistake the radio tower will stop glowing and won't light back up until the start of the next round. The compass points of the tower do not change. For reference, the north side of the tower always has a mahjong tile on the corner of the railings.

Step 8 is to melee the tower in the determined order.

Also, it does not have to be Samuel who hits with the galvaknuckles, it can be anybody.