This was all quite confusing, so I found a local guy that has a shop.
He tuned it within seconds, but agreed that it did have some issues.
He said the strings were too thick, they were raised too high, everything could do with some oil, and the nut and bridge was clunky.
So he’s gonna fix all that and I’ll have it on Monday probably 
Ah, good news Mikael! I think you’ll be very happy come Monday. Do let us know how you like your guitar after a trip to the guitar spa!
It will be well worth it. Nothing harder than trying to learn on a poorly setup acoustic guitar. While you are there, get the shop assistant to show you how to tune up your guitar. It’s something you will need to do before each practice session.
Good idea! I’ll ask him when I pick it up.
Sorry a bit late to this post but I will add what I would have said anyway.
When I restrung my classical guitar for the first time a few weeks ago which has nylon strings. I started to use my clip on tuner but it gave strange readings so I changed to a singing pitch monitor which gives a visual trace across all the octaves and used this to get close to the required note then switched to the clip on for final adjustment.
Must say I was little surprised but shouldn’t have been as I am engineer, how much more stretchy nylon strings are and how much longer it took to get in tune than the acoustic which I had restrung just before it, and had used my clip on tuner from the start.
Michael
Most nylon strings take a few days to settle in. Definitely pull them pretty tight on the peg before winding. Try to have as few winds as safe. Gently stretch them by pulling up at the 12th fret. I usually then tune up 1/2 to one full not and let sit over night (they will often drop a full tone) and repeat for a night or two.
This video by Mimmo Perufo is helpful for nylon. He is the main guy at Aquila strings.
1.) I have a battery-powered Seiko analog tuner that’s over 30 years old (used it for violin tuning daily). It has a cable input for use with an instrument with pickups as well as a typical mic. If used with the cable directly from the guitar, you don’t get sound effects from the amp/speaker that might impact tuning results. If someone’s tuner has this option, it might be helpful to use it. Many acoustic guitars have piezo pickups.
2.) I wonder how many people actually stretch their new strings properly after installing. Pulling each string up (not side to side) and doing this about three times for each string. Then, look at tuning and intonation.
3.) Opinion - I think it’s helpful to tune daily and precisely whether a novice or expert. This is a free and beneficial exercise to practice listening to pitch. The more I did this, the better I got to trusting my ear. It only takes 30 seconds.
Joshua @Jamolay
Thanks for the link.
Yes it took quite a few days before it stayed nearly in tune. I was a bit nervous about stretching the nylon strings, not sure why as I did stretch the steel strings as Justin suggested.
Michael