I'm going to address some of the problems people have had with the ending which I found quite logical.
(Most of what i will write is backed up by the audio recordings throughout the game, the rest are my theories).

1.why is Comstock old while Dewitt is young? are they from different times as well as different dimensions? (At the end of the game we find out that Dewitt and Comstock are the same person from 2 different dimensions)

Well the answer is that Comstock isn't old at all. The trans dimensional machine causes rapid aging and cancer tumors at prolonged exposures, and Comstock was exposed to the machine a LOT while "receiving his prophecies" (Looking into outcomes is actually what he was doing) ,so Dewitt and Comstock are in fact the same age.
And the exposure to the machine is also the reason why Comstock now (1912) has cancer.

2.why does Elizabeth/Anna have powers over space/time and trans dimensional travel ?

The answers is simply because she exists in 2 dimensions at the same time.
most of her is in one(Comstock Universe) while her pinkie was cut off during the abduction and is in the other(Dewitt Universe), and by existing in 2 dimension she sees (and can travel to) both of the dimensions and every other dimension in between (and because there are an infinite number of dimensions overall , there must also be an infinite number of dimensions in between the 2 she resides in).
but why can she also move threw time you ask? well time and space are one and the same, as was demonstrated by Einsteins special theory of relativity. so if one can move threw dimensional space, one can also move threw time.

3.How does killing 1 Dewitt before he becomes Comstock eliminates all Comstocks from all parallel Dimensions?doesn't that just kill the one Comstock and not all of them?

This is a Tricky one, bare with me!
The multiverse theory states that every choice that we make creates an infinite number of outcomes (or an infinite number of universes branching out like a ripple into the future) within those infinite universes created by the choice Dewitt made (be baptized and or refuse baptism) there are an infinite number of universes where being baptized transforms Dewitt into Comstock, and an infinite number of universes where not being baptized transforms The war veteran into a drunk single dad with a debt to pay.
So if we go back in time, and to the exact dimension where the choice was made ,and eliminate the choice before it had the chance to ripple out into the future, we ,in face, erase all the universes where Dewitt is a drunk and also all the universes where Dewitt becomes Comstock. (doing this also erases all "kidnapped as a baby" Elizabeth's) And by doing so making way for new universes rippling out of the moment Dewitt's drowns.(in those universes Dewitt Died drowning)

4.But it was the Dewitt from 1912 that was drowned by the Elizabeth's in the river, because they stepped threw a tare to get to the river. so is killing Dewitt 22 years after he was or was not baptized gonna eliminate Comstock?

Well, as far as i can see Elizabeth has 2 ways of trans dimensional/time travel.
A. physical travel threw a tare.
B. Fussing consciousness of a subject with himself in another dimension/time, without physically traveling to that dimension/time (Not unlike the time travel in the TV show LOST)
p.s- she can also combine the 2 ways.
During the game we see instances where Elizabeth unknowingly (the tower was not destroyed yet so she didn't have full control over her powers) uses the 2 ways together- for instance when they travel threw the tare in the prison to a parallel Colombia where Booker was a Vox hero we see founders that we killed back in the last dimension ,but not in the "Vox hero dimension" ,fused with they're dead selves and vibrate rapidly because they cant handle the "Schrodinger's cat paradox"(look it up) where they are alive and dead at the same time.

Soooo the Dewitt that was eventually drowned by the Elizabeth's is in fact the 1890 Booker Dewitt with the fused conciseness of the 1912 Booker (that's why he lets her drown him, because he knows what 1912 Booker knows)

5.What is this 1,000,000 lighthouses place? is it a real physical place?

I think it is. If there are an infinite number of parallel universes then everything that can happen does happen somewhere. If we follow this logic then there must be a universe where there is a sea full of light houses and doors, and self building wooden and stone bridges.
Elizabeth takes Booker to this universe in order to demonstrate her point.

6.What is this Constants and Variables business Elizabeth tells you about?

If you look at the choice that Booker made (be baptized or not be baptized- 2 paths) as 2 stones hitting the water, then the ripples that those stones will make intersect in some places, and don't intersect in others.
Now if you compare those ripples to the universes that where created because of the choice then they too intersect in some places (the same as each other= Constants) and don't intersect in other places (Different= Variables)
This can be seen ,in game, when the coin always lands on heads and not tales (when the Lutece's ask you to throw a coin) - This is a Constant.

7.What does repture have to do with anything?

Again, if there are an infinite number of universes then there must be a universe where a city under the water exists. and that is why in order to survive the unleashed songbird ,Elizabeth takes Booker and songbird to rapture, because songbird cant handle high pressure environments like deep under water, and she and Booker also need a place to breath hence the city.

8.What does the after credits scene mean anyway?

I think this is a glimpse into a "Perfect" Universe where Booker isn't a drunk(and has no debt to pay to anybody) or a religious zealot.
In that Universe Booker and Anna live happily ever after.
I think Elizabeth fuzzed Bookers consciousness with this universes Booker, at the moment of the drowning, and by doing so gave him a chance at a good life with his doughter.

O.k that's about it.
This was my take on the ending.
If you have more questions or you just want to say how wrong i am, feel free to comment.