Yes you can dissolve boric acid and adjust pH to 9.5 with NaOH, just be sure that you do not surpass your volume mark when adding the NaOH solution. This is, if you are preparing 1 L of buffer, first dissolve the boric acid in say 900 mL of water, add the NaOH solution not surpassing 100 mL to raise the pH. When the pH is set fill up to the mark. 

As for your last question I do not know your intended application but 0.5 M seems like a lot. 

Thank you for your response!

It is a lot. I am conjugating a carrier protein to 6kDa Dextran using squaric acid chemistry. The papers I'm basing my protocol on use 0.5M Borate pH9 for conjugation. None of the protocols mention adding NaCl, but it seems like it could be a reasonable precaution as I do not know how my protein will behave in 0.5M Borate. 

Do you happen to know the shelf life of Ammonium Carbonate Buffers? Should they be made right before use or can they be stored for some time? Does concentration affect shelf life? I hear they degrade quickly. 

Ammonium and carbonate will partition towards the head space of the bottle as ammonia and CO2, respectively.  Thus you can expect a decrease in solution molarity with time. They should be stored in a cold environment tightly capped. You must avoid opening them continuously as ammonia and CO2 will be released promoting more partition. My recommendation is to prepare them and use them right away.

Thanks for the feedback, I'll definitely make them fresh. 

I need to prepare 0.5 M of borate buffer with pH of 4.1. i have not fine any protocol. Please anybody help me.

Subash Chandra Bose I believe the pH of 4.1 is out of the buffering range of a borate solution.

Here's a protocol you can check out:

http://delloyd.50megs.com/moreinfo/buffers2.html