Q1. Yes that looks correct.
Q2. No the gross distribution will not go on Form 5329.
Q3. No do not enter anything on line 4a on Form 1040X. You will enter the combined gross distribution (from box 1 1099-R) on line 4 a of Form 1040 not Form 1040X. The combined amount from box 2a from the 1099-Rs will go on line 4 b of the new Form 1040. You will have a new Form 1040 with the changes that will be included when you send Form 1040X.
The amount from line 4 on Form 5329 will go on Schedule 2 (Form 1040), line 6. And line 10 from Schedule 2 will go on the new Form 1040 line 23.
You will use the new Form 1040 to help you fill out the amended tax return Form 1040X.
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