Yes, you can take all of you IRA RMDs from any IRA. Please see Can an account owner just take a RMD from one account for additional information.
Yes, you would enter $4,000 for step 3 RMD for this account.
To confirm, you have another 1099-R that covers the rest of the RMD? Here you would add the $2,000 RMD missing from the other IRA to step 4. So step 4 for the second 1099-R would be the RMD for this IRA plus the $2,000 RMD from the first IRA.
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