1) Are Standard Deduction, Personal Exemption, 401k Contributions and IRA Contributions exempt from all taxation (Federal Income tax, Social Security and Medicare)?
No, just federal and state. FICA (SS/MED) comes out of gross earnings. There are very few things that are exempt from those taxes when you have actual earnings from a paycheck. The few exceptions I can think of are Medical/Dental deductions for your portion of the premiums, and HSA contributions deducted from your paycheck.
2) How do you determine if IRA contributions or what percent of them are Deductible? (I know there are calculators and it's based off income & enrollment status in other retirement accounts but I want to understand how it is calculated)
You can deduct a Traditional IRA contribution if your income is below a certain threshold. See the link below for further details:
http://www.paychex.com/a/d/accounting/CCH_Fed_Facts_and_Figures_2015.pdf3) Are there any other major Tax deferment or avoidance methods that I am missing besides those mentioned above and things like tax breaks for children/dependents or FSA medical spending accounts?
HSA
FSA
529 plans for kids college.
4) If I change my 401k contribution percent midway through the year will my federal witholding be recalculated based on my new expected taxable income? or is that dependent on the specific companies payroll? Lets just say I haven't contributed to 401k for the first 6 months of tax year then I contribute a huge amount to max it out in next 6 months. Does my federal witholding go down to almost zero in second half of year since my new expected taxable income is 18.5k lower or does it stay the same and I get a huge tax return?
It will go down based on your new expected taxable income. If you begin on 7/1 and max out the $18K limit, so $3K/month, your net paycheck will only change about $2,250/month assuming you're in the 25% tax bracket. This is because you will not pay federal (or state) taxes on this income now, you will pay taxes on it when you withdraw it from your 401K/IRA.
5) I had a bonus (which i received only 2/3 of) and it was explained to me it was taxed differently (25%)+med+ss because it's a "supplemental wage"but is it taxed the same as other income come tax time? (Do i get a tax return on that bonus to make it taxed the same % as my other income that is not taxed 25%)
It all goes into your return to determine your refund/balance due. It will all go into taxable income, which is what ultimately determines the % of tax you will pay on it. The more tax deferral you do, the lower that tax % will be.