It sounds like you are on the right track here. Besides your mortgage, do you have any other debt? The mortgage debt at 3.5% sounds like a sweet deal, and I would encourage you to invest instead of paying down the mortgage. Giving your money time to grow (especially in an index fund or a solid, dividend-paying stock should easily beat the 3.5%
Here is what I would do, and I am probably considered relatively conservative by the forum's standards:
1. Get a 6 month Emergency cash fund. I would do this both to keep you afloat in case of an emergency and to keep some of your assets liquid so you can take advantage of an opportunity (stocks, rental properties, etc)
2. Pay off any debt over 4%. Now, it sounds like you might be able to just skip over this. If you are EXTREMELY risk adverse, you could consider putting some money towards your mortgage, but the numbers tell you to...(read on)
3. Fund that SEP-IRA. You've got this nailed!
4. Fund an HSA, if you can. I am just researching these myself, and I am unsure if they are available to the self-employed.
5. Start investing in a taxable account. Find a system that is comfortable for you, and commit to 'stashing!