Hey @SirWilliam, looks like we recently ran into the same issue (with dif size guitars and now scales/continuing normal routine)!
When I got my Taylor, they had a promo add a gs-mini for 1/3rd of what it normally costs. I didn’t anticipate how much I would love the GS-Mini or how convenient it was, especially with the backpack travel case. You could rarely find me without it my first month… if I left my house, it went in the back of the car. At home, always in my hands. The Taylor 414ce sat in its case unused… then I got a stand, and it sat on the stand in view unused. I had to consciously force myself to only practice on the full-size Taylor for a while to correct that. At first, things that I could play without thinking using the mini, I couldn’t on the full size because my finger muscle memory was just tuned to the smaller guitar.
Now, after a month of primarily using the full size whenever I’m home (gs-mini still travels everywhere with me), the full size feels more natural… I do get that same cramped feeling when playing the mini now. In some ways, it helped me - i.e., the first fingering Justin shows on the A chord, I just couldn’t do because of fret size, so I learned to barre the A chord with my index early on which really helped me with barre chords generally, and some other things like that… also the string gauge was a bit heavier (13s), so going to a regular acoustic was even easier (especially with barre chords) fretting on an electric feels like tapping thin strings now.
Regarding incorporating both - I’m doing this myself - it depends on how much time you have and what equipment. If you have a bit of time and want to have fun, keep in mind the pentatonic scales, etc., align with keys and chords… so if you have or get even a cheap looper (or have any pedals/modeling amp - it seems like 9/10 devices/equipment have some type of looper built in now)… Then, what I would do (and am doing) is mix the two. IE: Learning a song - record a chord progression loop, then practice the pentatonic/blues scales over it.
I got caught in the pentatonic rabbit starting last week and then felt a bit awkward going back to playing songs this week… but I was having fun mixing pentatonic and blues scales - ascend the scale pentatonic, add the extra bluesy notes coming back down. I was doing that for major/minor pentatonic over and over. Then, this week, experimenting with the major scales and triads and shifting to the minor pentatonic for the relative minor. All of a sudden, I was making my own music. I just grabbed a looper yesterday to combine the two and record simple chord progressions incorporating strumming patterns and other things I’m working on - or a song I’m learning… just the simple chord/rhythm vs., then practicing the corresponding pentatonic or other scales over it… which has the added benefit of allowing me to practice the practical application of scales early on, which will help it become second nature later (or so many far more talented, experienced players have told me). That’s my approach or how I’m trying to deal with what I believe is the same challenge you’re facing! If you end up finding something else that works, let me know 
+1 to the Ed Sheeran comment. He tried switching to a full-size acoustic for a short period a few years ago, then went right back to a 3/4 parlor. It’s just what he’s always used because it was convenient while busking and traveling, and it’s where he shines. Nothing wrong with that! I finally took the guitar I had for years out of the case and started learning after seeing him live 2 months ago. After his concert, I searched the whole house the same night until I found where the guitar had been stored. He is inspiring and just fun live.
. You can the revisit them later on in a more structured way via Justin’s program.