I have been in graphic prepress for a long time. Used Quark and then made transition to Indesign when it first came out. Now use CS3 for all print production, from hi end colour to newspapers. had a lot of teething probs along the way and have resolved most of them ourself.
I would be glad to help, if I can, with any of your issues.
From what i have read, the white lines are , or should be, only in the PDF screen preview, and not in the postscript code. When I produced a final PDF of my thesis, the images had white lines through then when viewed through Mac Preview but not in Acrobat. We used the see this in our newspaper final PDFs but once it got to the rip it printed fine.
One way to produce PDF is to 'print' (via the print dialogue) to a .ps (postscript) file and then run it through Distiller. This method is still used or favoured by a lot of prepress departments here in the UK.
As for image files we scale images in Photoshop to 110% of final print size at required resolution e.g. 300dpi or 250dpi etc. this ensures that there is optimum down sampling if the PDF is to be compressed. Otherwise we dont compress images for final output. Yes you get big file sizes.
We use a combination of Tiff for images or psd and PDF for adverts. psd is good because you alter the psd (layer effects etc) on the original and the placed file is updated automatically. Great for adverts.
Dont use png.
The PDF setting came be troublesome if not selected correctly and this depends on output device requirements.
having said that I thing InDesign is the best DTP software I have come across and I have really thrown everything at over the last five or six years.
Fell free to email me.