Unfortunately it's going to take a nice chunk of cash to make your 86 run like your Dad's 2020 GT.
Not that you can't improve upon the current power output and still have a blast with the 86. Most of what you stated from the shop sounds ok. Fairly standard upgrades and improvements. The TFS heads are excellent and do offer benefits with the 86 flat tops compared to standard inline valve heads. If you are not adding a camshaft then, it's not really a factor, but not adding a cam you are most likely leaving HP on the table. In regards to pistons the gentleman is incorrect. Ford offered the forged pistons in the Mustang from 1985 to 1992 when they switched to Hypereutectic pistons. The 86 are stand alone due to the flat top no relief design. Forged pistons are generally stronger than cast or hypereutectic and are often and upgrade made when rebuilding an engine.
As for the Cobra name plate, you pretty much covered most of it. My understanding is there's no real difference between your 86 Cobra and the US 86 GT model. The GT 40 intake is an excellent option, although there are plenty of options such as the TFS Track Heat and most likely could be less $$ than a true GT 40 intake. The Explorer GT40 style intake is another option, just know there are two types one with EGR and one without depending on your needs. In regards to clutch you pretty much want a stock or slight upgrade over a stock style clutch. Centerforce and Spec are my go to manufacturers in that regard. Centerforce has several options that keep the stock pedal feel, but improve performance. Most likely a Spec Stage One or at most a Stage 2 clutch will do all you need. Mcleod, Hayes, and Ram or other good options for a Mustang. The "Cobra" clutch kit was a good option for many years, but I know there was a quality issue for a bit, not sure if that has been fixed or not, but I haven't bought one in years.
As mentioned by the post above a rear gear change can also really wake up the Fox model Mustangs. I personally don't like anything bigger than a 3.55 rear gear ratio with the 5 speed as IMHO it makes first gear almost unusable when get any larger. The AOD cars generally prefer the 3.73 rear gear for best performance. Depending on what your current rear gear ratio is will help to decide how much of a improvement you will see. Good Luck!
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