Thank you for your many helpful comments! I will respond to some of them:
1. Try to give small and simple filenames in whole package especially cache folders and files which starts with %% etc and having long file name. Yahoo do not support unzip facility on its server. When you try to unzip it on system and upload it via FTP client, many files (cache files and some other) were rejected by yahoo due to their long and special file name (starting with symbols i.e. %% etc). the file names should be in simple alpha numeric i.e. cache 123 etc etc. Then the package can be uploaded to any server using ftp client.
Those files can actually be deleted/don't have to be uploaded. Everything else does, and their filenames are appropriately short. We have discussed disincluding cache files for future releases, and may do so.
2. Try to make the customization system more user friendly like phpbb3 (forum system). It checks the requirement itself and email customization is ultimate. It checks on its own everything.
During the instlall, OJS does undertake a system check, but it unfortunately doesn't check every single facet of the system before attempting to install. Our requirements are quite low, but sometimes even they aren't satisfied by hosting providers.
4. There should be system for font customization. There should be provision of manuscript to be converted to pdf or html on its own. It will be a very good option.
This will hopefully be more of a reality in the near future. However, you may want to take a look at the XML Galleys plugin, which can create HTML and PDF gallerys from uploaded XML files (NLM, or using your own XML and supplied XSLT). Again, we will be working towards improving this feature.
5. There should be a provision to index journal in famous engines like pubmed, scholar,JCR etc, as soon as issue published online
You can use the Pubmed export functionality to help you get indexed with Pubmed; there is plenty of information on the forum about this, I believe. There is also a plugin to help with DOAJ indexing, and of course the system works very well with Google/Google Scholar. Any advice in getting indexed in Scholar, JCR, etc. would be helpful.
Thanks again for the comments! If you would like to clarify any of the above points, please feel free.