My advice:
1) Open the Roth IRA with $5000 (the max for 2008). Use this as your emergency fund initially since you can withdraw your contributions at any time without penalty. Invest conservatively in a balanced fund like Vanguard Wellesley (VWINX). Even if you plan to eventually use this for your house down payment, with a 5 year horizon you cannot invest that aggressively. So maybe when #2 is complete you could go to a slightly more aggressive, like VBINX (60/40 stocks/bonds) or VWELX (66/33).
1a) Look into employer 401k/403b. Contributing 15% to retirement is a good amount at your age. This would be $6750 a year for you.
2) Build up emergency fund to $6K (3-4 months expenses in your case). Use a high-yield online savings account or money market. You should be able to get close to 4% right now. In case of a medical emergency you would use e-fund instead of HSA.
3) Contribute max to HSA if possible.
4) Pay off car if cash flow allows. Most likely this will not get done early if you follow the above. That's ok, the interest charges are not that excessive and it will be paid off in 2 years anyway.
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