In Mac OSX you can cut and paste sections from PDFs from the Preview app. I paste them into OmniGraffle and arrange by hand.
Under Linux, you could try converting the PDF to postscript (pdf2ps) then manipulating it with Inkscape. Or, you may be able to do it from a script using poster.
Alternatively, you could just save the image as a bitmap at the resolution you need, then edit the bitmap.
First, what you call paper isn't paper, it's a type of plastic! There's a possibility that it will melt if you try to transfer it using clothes iron.
Next, the document for the board doesn't mention that it's covered by anything, but if it actually is and you really want to use toner transfer, you'd need to get rid off the cover using developing solution. If you manage to get the real datasheet for the board, you should be able to get recommended solution there. I just use 10 g of NaOH in 1 l of warm water.
You also need to expose the board as well. First a quote from Wikipedia:
Photoresists are classified into two groups: positive resists and
negative resists.
A positive resist is a type of photoresist in which the portion of the photoresist that is exposed to light becomes soluble to the
photoresist developer. The portion of the photoresist that is
unexposed remains insoluble to the photoresist developer.
A negative resist is a type of photoresist in which the portion of the photoresist that is exposed to light becomes insoluble to the
photoresist developer. The unexposed portion of the photoresist is
dissolved by the photoresist developer.
You need to get documentation for your board or try your luck and determine if you need to expose it before developing or not. If you do need to expose it, just leave it in the direct sunlight for a few hours and then drop it in the developer. After it's developer, rinse it in water and the photoresist should be gone.
If the other side is not coated, I don't see a reason why it wouldn't work well for toner transfer.
After that, you need right paper, right clothes iron (or laminator) and right printer. That's why there are so many recommendations! Different combinations of those will provide different results.
I haven't experimented with magazine paper yet, but from my experience the thicker and glossier paper is, easier it will be to transfer the toner from the paper to the PCB. Also you need a good heat source to transfer the toner from the paper to the PCB.
In my experience, if you don't know what you need, go for FR4. Currently it seems to be the "default" PCB material.
Finally, since you said you don't have any resources locally and aren't in a rush, consider ordering a done PCB. It will be probably be cheaper than complete investment of making the PCB yourself.
Best Answer
Yes, you can use toner transfer to apply a silkscreen layer to a PCB. The toner itself is susceptible to removal with solvents, but either a thin layer of conformal coating or use of an additional substrate will solve this.