TurboTax didn't present the question that asks for your year-end balance because you did not continue through the entire 1099-R section. It's a common user error. Entering it directly on the IRA Information Worksheet accomplishes the same thing. Numerous times I've suggested to TurboTax Product Quality that they flag an error for an empty year-end value when Form 8606 is required to calculate the taxable amount of a traditional IRA distribution, but it falls on deaf ears despite the pervasiveness of the problem.
"By manually adding end year Trad. IRA, Part V line 35 (Conversion contributions taxable at conversion) auto populated the entire Pre-Tax amount that was rolled over from 401K to Traditional IRA, and the Federal Tax amount has increased considerably."
That's the expected result. I suspect that your Form 8606 and Worksheet 1-1 are now correct and there is nothing more that needs to be changed.
