Very good guide

Awesome guide. Seems you understand and play Heimer exactly like me. Good Job. :)

I've seen players rush turrets to 3, then max a ranged nuke, and that really doesn't appeal to me UNLESS you expect to be spending an EXTREME amount of time in laning phase. Having your turrets 1-shotted earlier in the game than they need to be is generally inadvisable.

You can pick up magic pen later with an Abyssal or Void, if what the enemy team builds warrants it. The Ionians gives you early CDR and of course the movement speed, which are both much more relevant to the "survival" style of play, and is much more expensive to come by otherwise. If people build early mag resist against you (which rarely happens), Haunting Guise gives survivability and pen to solve the problem.

The damage comes from the survivability- yes, you will deal lethal damage slightly faster with heavier AP, but if you're not living 3 seconds past laying your turrets, you won't ever reach that point. Since most teams aren't used to playing with Heimer, you have to assume that you'll need to drop turrets in the middle of a team fight in every game where you're not playing with a pre-made who knows how to play. When the big brain waddles up into range, people are going to jump on him not just because he looks squishy, but also because most AP carries tend to be squishy and build like glass cannons. Heimer can get away with building some survive over AP because the sustained damage from his turrets will make up the difference very quickly, whereas lots of other AP's have harsher mana or cooldown issues (meaning, they're higher burst but lower sustained damage).

Like you said, though, this style/build is definitely stronger for new summoners, but it's also better in "Tanky DPS" team comps than most other Heimer builds. And, of course, consequently worse in "poke" team comps. However, for most players, synergistic team comp is not even on the list of things they consider, so I reckon those points are mostly irrelevant.

The guide is amazingly in-depth (you wrote an awful lot) but it isn't very pleasant to read (yet), because they mainly are just walls of text. As the previous comment said, you should work on BB coding.
(For the numbered lists, you use [ *], for each point, if I'm not mistaken. Remove the space, of course.)

I do disagree with a few things: your choice for ionians and thus the lack of magic pen, and the fact that you max your turrets first. I think these things come down on personal preference though.

I also find that you will lack dmg whenever you play the meta (as ap-mid). In this case, you are usually the biggest damage dealer of your team in mid game and if you go too much survivability, you usually end up dealing very little dmg. IMO, ~400 ap is too little for an AP carry.

After these 'little' notes, I think you did a great job explaining heimerdinger to every level 1 summoner, really well done!

Thanks! I've now updated it with code links for most first-occurrences of things within the guide, and colored a few important lines.

I can't figure out how to make numbered lists work properly (even tried the indent that i found from googling, still doesn't work), any advice there?

This is actually pretty in-depth. +1. However, you only need one more thing to make it perfect, and that is to code. For example, Heimerdinger, UPGRADE!!!, etc. Refer to this guide for details.