You are making a fresh application following an earlier refusal. You want to know if you should submit only the evidence addressing the refusal notice or if you should follow the guidance.
Should I submit ONLY evidence to counter issues raised in 1st refusal
notice or I must include documents stated in the guidance
This may be in our archives, but it warrants repeating anyway. Each and every application put forward for a UK visa (of any sort) should start from square 1 and proceed on first principles. Assume nothing, take nothing for granted, and most importantly do not treat it as a 'formality'. It is an arm's length interaction with the British government, and even people who know the ECO personally will still treat the application with uncompromising sobriety and diligence.
Study the rules, study the guidance, review the application, and gather evidence to support all the points listed in Appendix V. Bank statements and other time-sensitive evidence should be up-to-date. Leave nothing to chance.
What should be the submit of my cover letter to explain reasons why I
shouldn't have been refused in the 1st instance.
This is a breathtakingly bad idea. The place to argue a decision is the Tribunal. They are not the Tribunal and do not need to hear arguments about how they made a poor decision. Decisions are audited and when they find a bad decision they will contact the applicant and invite a fresh application gratis. Trying to debate with them will just get their backs up and it can actually dig you in deeper if they spot an inconsistency.
There is no requirement to write a cover letter; it's an extra that people like to do. Professionals do it as a matter of client care, but again it is not mandatory. I still draft them for family and close friends and can promise that nothing much has changed despite the various rule changes through the years. A good cover letter in your case would open up with a restatement and clarification of the premise and then proceed to describe the changes in circumstances that govern this particular application vis-a-vis the previous one (even if the previous one was successful). And then close it out with a summary of how the applicant qualifies this time. That's 4 - 5 paragraphs polished down and honed. If it's longer than a page, then go cautiously, and if it's longer than about 1 1/2 pages it will end up being summarised by an assistant and the ECO will never see it.
If you think you will have trouble with the composition or keeping it brief, you can put dot points in the remarks section at the end of the application.
Tip: as we speak, they are rolling out a new system where people have to start coming in for interviews again (even Americans, Canadians, and other non-visa nationals who want an entry clearance). So you should prepare for that event also. If you need interview coaching or mock interviews there are some good professionals out there who can provide those services.