I don't think that's the problem.
I believe the voltage simply gets to low with most Nimh batteries and then simply refuse to go on.

You can have a look at NiZN batteries, they are rechargeable and have the same voltage as Lithium batteries.
Powergenix is a brand that makes them, very hard to get them in the EU but in the USA you can get them quite easy.
I'm thinking off shipping some over.

I think the K-r as a seconds doesn't make so much sense.
It doesn't offer anything over the K5 and the button layout is different.
The K5 and K7 have the same layout so easier to use together.
Also don't forget weather sealing, 100% prism viewfinder instead of a mirror viewfinder.

The Kr can take battery-pack as well, just like the K5 and K7.
And if you want you can use AA in an holder.

With hard do you mean the long wait?

NiMH would be the better one.
The camera looks at the voltage to see if the battery is empty or not.
So telling the camera what battery you use stops the guessing from the camera because it can guess wrong sometimes.

I would actually look for 50mm because with a 28mm you can get greater magnification but you also need to be very close.

I'm sure someone with extension tubes or a bellow can give you better advice.

That should indeed be correct 1/2 to 1/3 of a stop because those numbers 118R 118G 118B stand for neutral gray (18% gray) but light meters don't measure for that but for 12% gray, it has always been like that.
link

The ANSI standard gives exposure constant (incident light) 30 +/- 5 and that translate to 12.3% gray.

Don't forget you are also comparing two very different.
CCD in the K100D and the K10D and a CMOS in the K5.
They are build differently and work differently.

Like said can't comment on the rest, luckily Greg did that.

If you want the highest magnification you need to use wide angle lenses, the wide the lens the greater the effect the extension of the register (mount) has.
Something like a 50mm prime or 28mm should work just fine i believe and they are quite cheap to get.

Well you can always return the camera and ask your money back and then get it over 4 days again

Or just try to send your receipt to Pentax with the cashback offer filled in and see what they say.
No hurt in trying right?

Stand firm on the believe that you've the extra warranty though, i think like most companies they will try to get out off it
The DA*16-50 is a pro-grade lens so they are expected to last longer then normal lenses also.

Manual will work.
Tv will not work with any manual aperture lens because how can the camera adjust the aperture to match the shutterspeed???
And Tv with manual aperture settings is just Manual right
Av will work though, the camera keeps on metering and tries to keep up with the shutterspeed but it isn't as reliable as it is with auto aperture lenses though certainly not when you use high f-numbers from what i hear.

Never worked with bellows or with a grip so can't comment on that.