Wow, youve been through the ropes mate. But most of the kits need adjustments, thats just the way things are these days, and fixing them adds to your guitar skills.
So to your question about 2 kits and 2 separarte build diaries, yes that is a must, to avoid confusion. With your glue problems use water, although it can fur up the vaneer, or better still alcohol or thinners to see where the glue marks are first. TAKE YOUR TIME on every aspect of the build, there is no rush, and if you make a mistake and believe me you will, there is always someone here thats been there before and can help you.
Take one step at a time and dont try and do everything at once.
With the staining you can thin out the stain and build up subsequent coats, water based stains are better to work with as they dont dry as fast and you can correct your light or dark patches.
DONT use a furry rag or cloth, use something that wont catch on the grain. you can apply the stain with a brush or rag then gently wipe off with a clean cloth to get the effect you want. You can build up as many coats as you want until you get the desired effect..
It will dry lighter but go darked when applying the finishing coats to seal it.
You can use rattle cans, a brush or spraygun, depends on what you are happiest with. ALWAYS TEST THE CLEAR ON A PIECE OF PREPARED STAINED WOOD FIRST IN CASE YOU GET A REACTION. Then build up mist or thin coats instead of 2 or 3 heavy coats.
I use rattle cans with a handle and apply at least 30-50 coats. I know, over the top but thats just me. If you leave coats for longer than a day or so, finely sand between coats or it may laminate.
Most of the guys on here can add to this but this is just painting 101. All the best with your build..