Q:

Caulking a round corner stand up shower

I have to re-caulk a round corner stand up shower. I'm wondering the following:

Can I re-caulk it without having to take it down? The previous guy that came over, had taken it outside to clean it and brought it back in (kept it somewhat in one piece).
How clean is the surface supposed to be? I've so far scraped the inside (along the left, right and bottom of the rail) using a plastic scraper and some dissolving solution. There is still some residue remaining.
Lastly, there is a gap between the bottom rail and the floor base. How much space is normal? Are a few millimeters okay, or should the bottom rail be sitting flush to the bottom?

Update #1:
I'm now wondering the following: should I just get rid of the current one (barely 5 years old) and get a new one?
Shower itself:

Where it started leaking:

Noticed this (build up inside the rails) as I was trying to remove it, move it to the garage and clean it:

The build up is due to the ends being caulked I think:

A little history, this is a new construction approaching 5 years old. The original plumbers have had to come a few times to fix leaks on this very shower.
Noticed that the left "pillar" isn't tied to the bottom rail at all. Will have to redo the caulking on that panel as it has cracked while trying to take out the unit.
The walls aren't plumb it would seem. There is a noticeable gap in areas between the base and the rails.
Update #2:
Shower taken down and in the process of cleaning individual pieces.
Update #3:
Decided to lay the level on the bottom of the tray (left to right is from wall to center of tray):

Not sure if I should address it if it's off by this much? The rest of the walls are okay.
Also, contractor who built our house has been out of business for a bit now. The store where I assume he took our stuff cannot backtrack that far in the past. Having issues cleaning the parts, essentially a PITA.

A:

I have dealt with a lot of tub/shower surrounds.  100% silicone caulk (GE II is best at big box).  Most install instructions for the surrounds will actually tell you 100% silicone - some will give you their preferred brand.  
Answers:

You don't need to take it apart.  This may make it easier though.  Weigh how much time you will spend taking it apart and putting it back in.  
All of the old caulk needs to go and you need to be caulking on a very clean surface.
It should be sitting flush.  Why wouldn't it?  The fact that it isn't sitting flush tells me that it is moving (even if very slightly).  There is no way this 20 pound shower door is staying perfectly still suspended at certain points.  This movement will cause constant issues with your caulk and the fact that it will cause the issues in the easiest place for water to get in is a double whammy.  It isn't hard to install these things right.  There is no reason this should be sitting right (if it is bent then it needs to be bent back).

Other notes:

Sorry to say but this whole job looks hack to me.  I am not sure about the "main" issue (other than the people working on it) but it looks like maybe the wall isn't perpendicular or base isn't flat.  
On the last picture it looks like you are actually missing a trim piece on the inside.  You must have something there to salvage this shower. I would simply call the manufacturer.  Ask them if they make something or have replacement parts for your shower.  You might want to order a new enclosure.  Your actual shower looks fine it is just the door system so I don't think this is a tear down for sure.
The caulking looks ridiculous.  This is "one-month" caulking.  More caulk isn't better.  The more caulk you apply the greater chance of the caulk being moved, bumped, whatever.  Then the seal on the caulk will break and a .5 mm crack can allow tons of water to leak.  Also all of your caulking should be from the inside of the shower.  Anything on the other side is cosmetic.  

