First off, BRAVO !!! ... for a topic that is developmental coaching.
Table Tennis Forums neve have enough of these topics, you rarely see them.
Also, Bravo on achieving your current good play level, many never make it to where you got starting as an adult.
Since there is "No ONE Way" in table tennis, but many ways, it would be a book of a reply many of us would have to write.
You expressed a few concerns and I will address them in general.
Your concern about no being able to hit through certain opponents... my reply would be to not worry about that. When you timing and seeing the ball gets better, you will do better there. If you are close to the table, you are taking ball earlier and pressuring opponent with quickness. This is successful at a 2600 level... it can still work for you. As long as you are able to make the opponent wonder where the ball will go, you have the edge. Of course you have to be able to hit all the zones with consistency, but that is OK. Being able to pound the middle pays off more than hitting through people... and it also opens up the corners.
Executing a counterloop finish vs a slow, heavy incoming ball while parked at the table is a skill some 2400 level players suck at still... don't sweat it yet. Still, if you know what to do and are not flinching from the long swing... you can put away those balls. The trick is to recognize early what happened. A slow, heavy topspin ball is like a freezing time warp. If you are not caught mesmerized, you have time to setup and act. You have a small window of space to execute the shot, so your position must be right. If you are gunna pound the ball, you are making a step in on a shallow ball, or for the ball landing deep you are crouched and exploding forward. You goal is to impact the ball on the rise at a little over net height (or higher if it is a more high arching shot) You will be covering the ball, but not totally. How much depends on the incoming spin and vertical angle. You will be swinging forward, using either legs/hips to start explosion or a step in. You will be impacting the ball over the table for a shallow ball, or near/just past/just in front of endline for the longer landing ones.
You have three kinds of impact that will get the job done. You can go forward into the ball covering it and maintain the loose grip. You accelerate like the other shots, but keep the grip loose. This will not give you a big finishing power, but if you go in to meet the ball, it will be easier to get the timing to meet the ball. This is critical, the timing. It is hard job to get timing right and pound the ball 120% consistently while you are learning this, that is why I recommend a progressive approach.
Critical points - recognize early what happened, don't panic, take mini steps/hops/slide/whatever to get into position, see level of spin on ball/the arch/the landing spot, crouch and then explode shortly after ball lands, impact on rise above net, use the grip pressure you have adjusted (very loose early while learning - very firm at impact when timing is learned)
The soft grip early will make it easier to focus on the timing of meeting the ball as you are not worrying about hyper explosion... you will be able to easily return the ball, and often, the medium pace you generate will be enough to finish the point. Many players will be amazed you countered their heaviest, best shot. You will still be in position to deal with any return. Often, there won't be a return.
The goal is to get the timing and the other stuff right, and when done at a high consistency, increase grip pressure at impact progressively to the point where you instinctively firm up the pressure right at impact. This will produce the most powerful transfer of power to the ball. This kind of impact (loose, then sudden firming right at impact) will cancel out whatever is on the ball and make your own spin, plus produce loads of power)
The other way is to impact the ball a little on the side, just like you do for a "Hookshot". Impacting on the side makes the incoming spin bite much less on the ball, plus it allows you to easily add you own spin. This is AWESUM for control. Early on, when you are learning the timing and impact, it is important not to miss and be consistent. This kind of impact makes it easy to control the ball. You can use the variations of light and firm grip pressure. A lighter, real loose grip will allow you to corkscrew/side/top spin the ball very short near net landing well wide and short of FH corner while breaking away from opponent. Even if this return is not very fast, it is a point winner. A firmer grip at impact allows you to make a return of a fast loop loaded with spin that lands at FH corner and breaks away... that is also a tough shot to cope with.