What is the best/ethical way to estimate code clean-up? [duplicate]

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• How can I quantify the amount of technical debt that exists in a project? 11 answers

I have been working on a product line since my senior year of college for my current employer. Now several years out of college I am in a position where I am giving estimates for change requests on this same produce line. Please note that our software lead still approves the estimates, but is hands off during the process.

As my skill set continues to grow, I continue to see things which I can improve upon. The issue is how to get these changes funded. My current process is to clean up / refactor code if it touches an area that has an active change request. However the dirty sections of code that aren't part of an active CR are neglected and bug me more and more as the product line matures.

To help clarify, I do not believe that the customer should pay for a full rewrite of the software, unless it is in fact cheaper to do so to meet new requirements. I do prefer the incremental changes to clean up bits of code.

When submitting quotes / estimates, what is the best way to ethically try and recapture the costs of code clean up?  

To elaborate further, what kind of padding is typical for general maintenance? Should it be based on lines of code, project complexity, or some other metric?