1) My mast has the flapper piece at the hook and I did struggle hoisting and latching the main sometimes. Should I remove it or not?
Dremel it off, leaving just the hook.
Then make sure you have a halyard ring (looks like you do), when standing in front of the mast about to connect the ring to the head of the main, let the main halyard hang naturally, then twist it four or five time "away" from the side of the mast that has the hook. Then as you raise the sail the ring will automatically want to twist back toward the hook at the top. If you get this right it will hook first time every time. (this assumes everything is in working order)
To unhook, disconnect your rotation limiter and downhaul, then raise the sail off the hook by pulling on the main halyard, keeping tension, rotate the mast using the rotation limiter away from the hook, release the halyard and you are unhooked.
2) Other than shroud anchor pins, what else should be replaced? The rigging looks great but how do I tell if I have the updated crossbar anchors?
Inspect everything, compare your boat to the assembly manual and parts catalog, make sure everything matches. Furlers sometimes need to be rebuilt. Check the plastic pulleys the main halyard crosses at the top and bottom of the mast, if they are rough can make it harder to raise the main.
Jib halyard, the jib halyard with the sister clips makes it easier to raise and lower the jib. Make sure you understand how the jib halyard is supposed to be run.
I have the pop in port hole caps but they should be fine for light wind lake sailing.
Replace those, it's easy and the pop-offs leak, even from rain if they are old enough.