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If you rollover a 401k into a regular self-directed IRA (so you can invest in individual stocks) are you subject to the $2000/year contribution limit?

Rollover is not part of the $2000/year contribution limit. There's no limit on the rollover amount if it's from a qualified retirement plan like the 401(k).

Will I have to pay taxes on any amount over $2000?

All rollover from a qualified retirement plan are not taxed. However, tt is considered a distribution, so you will need to enter this amount on your tax form.

Do I need to use a Rollover IRA for doing this? I have no plans to later return this money to an employee sponsered 401k.

There's no such thing as a Rollover IRA. You must rollover your retirement account into a traditional IRA. If you plan on rolling over that into your new employer's retirement plan, ala 401(k), then that traditional IRA, call conduit IRA, must be separated from all other IRA; i.e., if you're planning on rolling over from a 401(k) to a conduit IRA to a new 401(k), then those amount can't be co-mingled with your other IRA.

Also, I am aware that if instead I wanted to rollover my 401k into a Roth IRA that I first need to move that money through are regular 401k.

I think you means traditional IRA, not regular 401k. To get money from 401k into Roth, you need to rollover the 401k into a traditional IRA. Then convert the traditional IRA into a Roth IRA

If I take this second step and move my money onto a Roth IRA am I subject to the contribution limit?

The conversion amount is not part of the contribution limit. There's no limit to the conversion amount. However, in order to convert from a traditional IRA into a Roth, your modified AGI must be under $100,000 (single or married jointly. You can't convert if filing married separately). The modified AGI is your AGI less the conversion amount plus the deduction for contribution to the IRA plus some other type of deduction.

Will I have to pay taxes on the total amount of money that I rollover?

The conversion amount is taxed as distribution, e.g. as ordinary income on the taxable amount. However, you do not have to pay 10% early withdrawal penalty.
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