1. For the rest of this year are there any options to sock away monies pre-tax since I can't really contribute to the new 401k yet? I can do a FSA so that's a little bit but not near enough. My AGI will allow for after tax / Roth IRA.
TomTX gives good advice.
Just be sure that you are good on the differences between FSA and HSA. An FSA only lets you roll a small amount of money from year to year. An FSA isn't the beautiful medley of tax-avoidance/deferral + investing long-term that an HSA provides. So, if you only have an FSA, make sure you don't put more in it than you can spend this year.
You may know all this, but it will also serve as a warning for others who stumble on this thread.Did you want to sock away some money this year for kids' educations? That would at least save you some state taxes this year (assuming you live in a state with income tax that lets you deduct 529 contributions), and the earnings would be tax-free on federal.
As it seems the investment advisor is not really sure on your company's plan ("if the program allows it"), you should really nail down these details before you make a decision. If the plans allows in-service distributions, my understanding is that you can immediately roll contributions into your own IRA accounts. This big rollover thing the adviser mentioned is sometimes called a Mega-Backdoor Roth, so use that term to start your research.
Bogleheads Wiki - After-tax 401(k) (see also links at bottom of page)
Bogleheads Forum - The Mega Backdoor Roth IRAIf you make your contributions, have them set to go to the settlement account/money market, and roll them out to an IRA the same day or next day, the expense ratios in the 401(k) won't matter because you won't be investing in those funds.
If you are currently a "highly-compensated employee" for 401(k) purposes, you may need to factor that into your considerations, as you will be limited in your contributions by the actions of less-compensated employees at your company, which may require contribution clawbacks.
Again, before you make any decisions, look into the costs (and paperwork!) for each option. If you go the contractor route, you will have to factor in payroll taxes as well as all the benefits your company currently covers (health ins, life ins, disability ins, unemployment ins, etc) before setting your rate.