I'd also say, since you're talking about not getting a job because of your inexperience with MySQL, you almost certainly should do as others are saying and start using a framework. I didn't realise you were applying for jobs. Almost no company is likely to employ somebody who always wants to re-invent the wheel. Part of being a programmer is learning to use the right tool for the job. You'll do yourself a big favour and your (potential) employer a big favour by biting the bullet and using other people's code.
Everyone specializes in different things. You don't have to be able to write a framework to build a CMS. The point of a framework is not to do that work for you; it's to give you the foundations to build from. You still have a lot of work to do if you're building a complete web application in ZF.
I'd also be surprised if most employers will be looking to see that you have experience in one of the mainstream PHP frameworks. I've been to quite a lot of interviews and interviewed people myself and I know from experience that being comfortable working with a framework is almost a requirement. Frameworks promote good programming practice at the end of the day.
I'd suggest that you download Zend Framework, stop trying to re-implement things that you don't need to re-implement and actually start building a real application in a framework, adopting design patterns that fit your needs as you do so. This in itself will be much more valuable experience if you're applying for a job than if you know how to build a request router.
What sort of questions do you expect to be asked at a job interview? They're not likely to ask you if you can build a request router. They're also not likely to be interested in your one-dimensional directory layout. They're likely to ask you about problems you've faced and how you've solved them. Things you find the most challenging. Where you might apply particular design patterns. What frameworks you have used. What tools you use in your workflow. Very general questions that I'm guessing you're not equipped to answer if you always avoid making use of the tools available to you. You're an engineer with a great big toolbox, so start using it