I made the same switch a few years back. I started on fretted electric in 1980, took up DB in 1992 and pretty much discarded fretted bases for a while (and sold my fretted 4001 in 1997). Then I got a FL electric in 1999. It wasn't until about three years ago that I bought a fretted bass. At first, I had the same issue with "fretting out" and such.
The solution is simple: don't think about intonation at all. I know this is counter-intuitive after years of DB playing, but try to look away from your fingers for a while and just finger the notes wherever you want. Once I conquered this hurdle, I found fretted playing to be a breeze compared to what it used to be. Remember, you likely have pretty strong hands and fingers from playing DB, so just fret the notes anywhere you want in between the two frets. Forget about technique for a little while. Soon you will adjust to a nice compromise near the fret but not on it.
And not to worry, I go back and forth between fretted and fretless all the time and playing fretted this way hasn't affected my intonation.
Best o' luck!
Tuning a mellotron doesn't. - Robert Fripp