I struggle with the same thing. A few tips from what has worked for me.

First off, if the song is on GT then it's easy to loop the challenging section of a song and play it back at a slower speed. I'll do that a dozen times or more until I feel like it's in me. Then I come back the next day and do the same thing. It's amazing what happens overnight or even after a couple days away from a challenging section.

If it's on youtube or eslsewhere I try and get an mp3 and slow it down with something like this free online tool. But no looping. So, this just takes doing what we used to do with tapes: play, rewind, repeat.

Maybe someone else can answer better, because I struggle with counting, but, if you can figure out the count for the section you can set a metronome to a slower bmp and practice playing the part with counting. Maybe it's highway to hell, for example, and you know the openning riff comes in on the and of three, set a metronome and practice that.

It seems I struggle with the timing of at least one section on a song I otherwise nail and I find it hard to isolate and practice that section. Mostly I just end up doing it a whole bunch until i work it out.

Another suggestion is to try software like Guitar Pro 4. Most songs can be had for it and it has a click and will look a section of a slong at a slower tempo.

Hope that helped. I hear you.