From the FAQ (i.e. official errata):
As per the rules on size changes, size changes do not stack, so if you have multiple size changing effects (for instance an effect that increases your size by one step and another that increases your size by two steps), only the largest applies. The same is true of effective size increases (which includes "deal damage as if they were one size category larger than they actually are," "your damage die type increases by one step," and similar language). They don't stack with each other, just take the biggest one. However, you can have one of each and they do work together (for example, enlarge person increasing your actual size to Large and a bashing shield increasing your shield's effective size by two steps, for a total of 2d6 damage).
So Improved Natural Attack feat, Improved Damage evolution, and Impact amulet don't stack with each other. Large evolution and Enlarge Person don't stack with each other. But you can take one from the first category and one from the second.
Now, despite what the rule actually says, it's possible that it wasn't intended to work that way. Prior to this FAQ, the rule was "Multiple magical effects that increase size do not stack." (quoted from several size-affecting spells.) Under that old rule all of your mentioned abilities would stack with each other because most of them are non-magical. The FAQ both added the clause about effective-size-increases (which is clearly the main point of the FAQ), and removed the "magical" qualifier. I'm not sure whether the latter change was intentional, or just sloppy wording from the FAQ author.
Yes, but with contingencies...
So, first off, I will say that these will most definitely stay relevant. As the rogue, when you get into higher levels the ONLY way you stay relevant is doing the stuff other party members can't. Pathfinder isn't as bad as its DnD 3.5e roots in this line, but Rogues are still far less powerful than many other classes in a "traditional power" sense.
That said, your goal, again, is to do what they can't. What you do best is take out people that would pose serious problems. You are the master of 1v1 stealth attacks, the "getting the final killing hit in a hard battle" person.
For that, these abilities do stay relevant. Ranged Touch SA, for example, are drastically underestimated, but especially vs tanky opponents they can be a huge boon because you can bypass normal defenses.
As a Rogue, you want to aim towards "toolboxing" yourself a bit. Toolboxing refers to the idea of having an good answer to many problems as opposed to a few ridiculously powerful answers to a few problems. These things you are looking at help you do just that.
As a personal note, yes...you will lose straight up melee power and SA damage of dual-wielding rogues. That's fine, though...that isn't your gimmick, and in my opinion it is a waste of rogue potential. You, however, are swapping that pure damage for a rather nice set of utilities that enable you to penetrate defenses, deal damage, stay alive, etc.
Also remember that higher-level encounters will generally go quickly with a good party, so things that can't be used often have more weight because you don't need to worry about 5 rounds of trying to deal with a random enemy like you do at lower levels.
From the perspective of a person who enjoys Pathfinder rogues and rogue-likes, I can say you definitely are making a good choice. Just make sure you play to these strengths and don't go after the same format as those stereotypical two-dagger users. ;)
Best Answer
Your damage does not increase by level. (1)
(1) At least not directly. You get more feats, hit more often, have higher base stats, may aquire magic items and get stronger spells. But the raw damage does not increase. If a weapon does 1d6 damage, it does so, regardless of your level. Exceptions will be noted in the damage text.