Newbie Question

Ah, OK - yes the access lids are the "inspection lids"... or pie plates. You're good - if you had eyes in there and no more water was running into the aft bilge from the forward area of the bilge, then you're good.

Yes, very normal for boats with floors that are close to the waterline to have water come into the boat when there's extra weight on one side of the boat while at rest. Nothing to be alarmed about - it will all go right back out again.

New flappers may help alleviate that... but it can still happen with new flappers - they are more designed to help keep water out when backing down.

You don't have to move any batteries - just put someone that weighs between 100 and 140 pounds at the exact spot on the other side.
 
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Brilliant! TY: "You don't have to move any batteries - just put someone that weighs between 100 and 140 pounds at the exact spot on the other side."
 
Perhaps a seacock is open or not seated properly. If the plumbing going from an open seacock to a livewell or other output is broken or leaking, that would put water in the bilge.
 
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Definitely doesn't look like a difference of 4"-5" or close to it, looks more like maybe 1"-2" at the very most. I'm guessing it's because you've got both batteries on the starboard side and that's the reason why it lists a bit to the starboard side. If you're ocd and want to "fix" the problem, then separate out the batteries and put one on the port side. If not, I doubt this would cause any sort of issues other than strictly appearances. Does your boat have trim tabs on them? If so, you could always adjust the one on the starboard side down a bit, which should lift the stern on the starboard side up some. Otherwise as mentioned above, just use the boat and have fun with it.
 
The water that pumps out when launching the boat but didn't seem to be in the bilge is most likely water in the forward bilge area. This is very common for V hulls. That is normal but annoying. That said it would typically be symmetric and not cause listing. The gas tank coffin may be filling with water. If so, that needs to be addressed. The drain tube/rubes for the forward bilge area to the aft bilge may be clogged.
What size and quantity of batteries are in the boat and are those figures different than the original build (especially battery size)?