Ok so doing research, we are both right and wrong. The 289 block had a few different wall heights. The C5 block was the shortest, the C6 and C8 blocks had longer cylinder heights. It's not that the 289 can't be stroked to a 331, it's about cylinder wall integrity. The pistons tend to side load in the cylinders. And I misspoke about the stroke measurement. Being that the 289 has a 4" bore, a 3.25 crank will give you 331CI. Sorry, it's been awhile since I was really into small block ford performance.

As far as your pushrod length, you may need to get an adjustable pushrod and order custom length ones. I don't think one solid tapped lifter costs very much.