There is a 99% accurate bijoy > unicode > bijoy converter. Here's the link > http://bnwebtools.sourceforge.net/
There's also two type of text in bijoy
Bijoy 2003 Type
Bijoy Classic Type
So those text which are in SutonnyMJ but still broken in some alphabets is because of Bijoy Type Version. You can convert that text from 2003 to classic. Which will solve your problem. To convert the text between bijoy versions You have to install Bijoy Bayanno 2012 version on your machine. Then you'll find a converter add-on in Microsoft Office > Add-Ons > Bijoy Classic Converter.
Just paste the text in Word, convert it with the add-on then use the converted text in any application. eg. Illustrator, InDesign etc.
You're using Unicode Text that's why the client reported the second problem. You have to convert the text to Bijoy ANSII using the converter I mentioned earlier. Then use in any application and if then alphabets breaks you have to convert it between bijoy type version using the add-on I mentioned earlier.
You can also change the Bengali Font, there's a lot more than just the SutonnyMJ. You can try KarnaphuliMJ, KongshoMJ, JomunaMJ, KalindiMJ etc.
I would love to help you further more in this matter, if you need to.
Web & Graphic Designer, Photographer