"Now my CPA, put this excess withdrawal of $6,043 as taxable income in 4b of 1099"
That's wrong. Only $43 should be on line 4b. It seems that the CPA failed to include the $6,000 of Roth IRA contribution basis on Form 8606 line 22 to be subtracted from the $6,043 distribution. Your CPA needs to correct this (and should not charge for correcting the mistake).
Form 5329 Part I should show a 10%, $4 penalty on the $43 (I assume that you are under age 59½) and Part IV should show the $$6,043 distribution being subtracted from the $6,000 excess, eliminating the excess.
