Might want to save yourself a bit of work and trouble by either a) using JE-Comics Converter to convert your image files to a viewable PDF, or b) use PDFRasterfarian to convert your PDF'd mangas into an optimized Sony-native LRF format.
I've converted quite a few manga comics for use on my Reader by actually using both in conjunction with each other; JE-C converts my jpg & png's to PDF and PDFR converts it to a smaller and optimized format for my use. I personally like them both (as you can tell) and each does what it advertises quite well, I just like the final output of using both. Using this method, I have converted several mangas and have already read a few as well.
Pro's & Con's:
JE-C stitches together your directory of images and resizes them to the appropriate size for viewing on the Reader, only downside is the size of the resultant PDF; which is a function of the PDF format and not JE-C.
PDFR optimizes your PDF's for viewing on the Reader and applies a few filters/enhancements to improve the output quality on your Reader. ATM it cannot stitch together the jpg/png's like JE-C, but it is mentioned that this option may be available future versions. Another upside is the size ratio to a PDF; e.g., coming in a roughly 1/2 to 1/3 the size of the original PDF.
Quality is excellent with both, but I think PDF-R applies a few more edge filters to enhance the text of the final product. (Maybe you two alex_d & kirys should corroborate with each other and have a joint venture? Either way, I'll still continue to use both your programs.)
Edit: Sorry
Kirys, I suck with names and should have checked first. Updated above so there's no more confusion (yikes, I'm so embarassed!

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