Possibly, if you can retrace what has been done to add iPad 3 support between 0.99.5 and v1.0.1. You can use the github commit history. Though this will not be an easy task, and possibly cost you more time than updating to v1.0.1.
Why would updating be a colossal task? If you tried it and found hundreds if not thousands of errors, this does not mean you'll have to apply the same number of fixes. One renamed cocos2d class can already give you dozens and more errors depending on the class and your project.
To update cocos2d follow the steps described here. Especially important and often forgotten is to actually delete all the old cocos2d files, otherwise you may still be using old version source files in your project causing all kinds of trouble.
From what I recall when I updated the first edition of my book (cocos2d 0.99) to the second edition (cocos2d 1.0.1) there was very little code between those two cocos2d versions that actually forced me to write new code. 99% of the changes are merely renamed classes, methods and properties - renaming them accordingly fixes 80% of the issues, and the rest are new or removed or re-arranged parameters of methods, almost as easily fixed though not as easily because you can't always use refactor respectively search & replace to fix those.
I suggest to fix the easy ones first (renamed classes, methods, properties) and then get to the rest. If you need help, you already know how to use SO. ;)