I recently paid off my $22,000 student loans @ ~5.5% fairly aggressively. My reasoning was influenced because I had a well paying job, but lacked job security. I wanted to know that I had enough savings to get me through a possible union strike and later layoffs, and I wanted to be as free as possible from my student loans so I had fewer required expenses to manage. I didn't have a mortgage, but I would probably do it the same way again if I did.
Here was my plan, executed between Jan 2013 and May 2014:
1) Made sure I was contributing the matched amount into my 401k and saved 2 months of income. This was before I read MMM, but I was naturally rather frugal. This mini E-fund was meant to tide me over for a union strike, but was not a long term emergency plan.
2) Put my loan payments on auto-pilot for minimum amount. My lender offered to lower my rate by 0.25% simply for signing up for direct payments, so that was a free money no-brainer. It doesn't sound like you have this option, but it never hurts to double check.
3) Apply extra money to the loans every month except for a set amount to the emergency fund. Everything was tracked in Mint. I don't keep a strict budget, but I do have a solid idea of my expenses for the big three: Housing, transport and food. I set aside a small set amount to gradually bring my emergency fund past the 2 month minimum I set (shooting for 6 months). This is about the time I started reading MMM and realized I can increase my payments even more and decrease my expenses a lot.
4) Pay loans like crazy and start to cut expenses. After my automatic minimum payments went through, I'd apply the rest I had allotted into the account. All extra money went to the loans. 3rd Paycheck in the month? Student loans. Tax Return? Student loans. Birthday gift? One humble dinner out and student loans. This pushed my payment due dates out by at least a year and paid off a bunch of the loan. It also got me adjusted to living on a small amount of my income. I got about halfway through my loans this way.
5) Find out there will be layoffs in late 2013 and begin to realize the value of having FU money. Adjust payment schedule to allot more to savings to give me a bigger emergency fund and pay slightly less per month to loans (still way above minimum).
6) Meet my FU money goal of 1 year expenses. Dump money into loans again. Apply all gifts, tax returns, and windfalls to student loans in Jan-Mach 2014. Pay off $11,000 in three months without touching emergency fund. Kiss Sallie Mae goodbye.
6a) Immediately max out 401k to prevent lifestyle creep. Adjust W-4 statement because I was over paying taxes. Set up vanguard account. Watch as my stache grows exponentially because I am saving all the cash I was sending to my loans.
When I found out about layoffs, I did the math and tried to figure out the cost of my different scenarios. In the end, it would have saved me ~$700 in student loan interest to wait to build my FU stache, but emotionally it was a better choice for me.
Regardless of job security/mortgage/whatever, I feel that the trade off of your leveraging option isn't great when your interest rate is over 4%. Like you mention, there's no guarantee of growth in the investments that will beat that rate, and this debt is a psychological burden for you. I also agree with rmendpara, keeping loans for the tax deduction is a poor trade off. Better to double check your exceptions on your pay account and make sure you are as close to perfectly paying your taxes rather than hoping for a big return (which is losing you interest money for every month you wait to get it back).
Out of your given options, I also support #2, but I wouldn't get rid of your emergency fund. I just read your reply and that actually sounds pretty reasonable. If you feel okay doing the "credit card as emergency fund" for a short time, it's a gamble, but might work okay since you have a fairly low-risk lifestyle other than your mortgage.
I wouldn't worry to much about the delay you will see in retirement savings while you pay down your loans. If you run the scenarios mathematically, it won't affect your FI date much. I did this and it made less than 1 years difference using a rough approximation. However, having no loans is a HUGE weight off my shoulders. Good luck!