خب با توجه به متن پیام استاد ، فکر کنم همون متن خودتان با کمی تغییرات به شرح زیر مفهوم مورد نظرتان را به استاد مربوطه منتقل کند :
With thanks for your message ,I should give you my apologies for the shortcomings you found in first and second pages of the said paper. In fact , these are my problems too from the side of the co-authors of the manuscript.
However,after I finish my part of the paper I'm looking for and will indeed much appreciate a good idea for improving the manuscript. I am really really thankful to you for your kind favour and helps and also taking up your precious time to read the manuscript.
I will await for further news from you accordingly.