Just in regards to gaining levels without gaining perks:
Ive had the same thing happen to me.
I enabled both the stat and exp doubler, and sometimes I'll gain levels without that stage's perk point appearing. seems to happen inconsistently though. I've only had it happen with attributes rather than skills though.
Ive seen it happen for agility, the main level, and vitality.
I think it might be that I enabled the 'unlimited perk points' option and may have left it on while continuing to gain levels. I'm not certain of this though.
Currently Im on main level 17 with 0 perk points, and none of the perks past level 4, since I seem to be gaining levels without the corresponding perk points. I am aware that you don't get them every single level, but there should be a good many more.
unfortunately theres no option to set the main level, so I'm not able to reset it to 1 and gain an extra perk point that way.
[Edited by bodine_wilson, 2/16/2018 9:02:51 PM]
The main level is an average of the other levels, so you don't have to edit that, you just have to change the strength, etc, to lower levels, and it will automatically change your main level too.
Unfortunately, editing your stats (or just cheating for XP and getting them to shoot up quickly) seems to break your Main level.
You can have 20 in all stats, but for some reason be stuck at Main level 19, without any way of increasing it.
I think it has something to do with the 2 stat increases you get at the start of the game. When you use the trainer, the game seems to forget about those, and your main level actually drops slightly because of it. So if you take a point of Strength at the start, and use the trainer, it will end up negating that point. So you would start with 2 Strength instead of 1, which starts off calculated into your Main Level. But with the trainer, it doesn't seem to get calculated properly.