1) Those aren't regulations, those are statutes. It is disturbing that you are attempting to advise people on this subject but do not know the difference. Statutes are written by Congress, regulations are written by the Treasury Department to implement or clarify statutes.
2) The PDF is for the 2004 version of the R&D statutes. They have been revised significantly since then.
Cornell is not an authoritative source but it's easier to read than the GPO website. If you want final authoritative sources, you'll need to read the House and Senate resolutions and to track down a physical copy of the appropriate issue of the Federal Register.
It really is a shame that this accountant person is tripling down on everything without actually having the needed domain knowledge.
Thanks for following up on each of these -- as a small business owner that might pursue this, it's often difficult to separate signal from noise without having much time to spend on it.
2) The PDF is for the 2004 version of the R&D statutes. They have been revised significantly since then.
3) Current version of the statutes: https://www.law.cornell.edu/uscode/text/26/41
Current version of the regulations: https://www.law.cornell.edu/cfr/text/26/1.41-1
Cornell is not an authoritative source but it's easier to read than the GPO website. If you want final authoritative sources, you'll need to read the House and Senate resolutions and to track down a physical copy of the appropriate issue of the Federal Register.