Don't be sorry about asking questions, that's what the thread is for.
First thing first - RPG & SDHQ - those numbers are correct (as advertised - real numbers achieved I can only speculate) BUT they are not for the parts I listed. Those are the advertised travel numbers for each companies LT kits. The parts I showed in my post above are Raptor spec (width) and will only achieve ~14" of travel with front axles installed - you might be able to get another 1" or so without front axles. The travel number for the Dirt King MT setup is correct (even though they advertise it as a LT setup, it's MT).
You are correct, you need the appropriate UCA for whichever LCA you buy - IE, if you buy a Raptor spec lower, you need a Raptor spec upper. If you buy a Raptor +2 lower, you will need the matching upper and so on. I wouldn't worry to much about this though, the LTs are sold as kits with all matching parts anyway since they are typically fabricated either in house or from a dedicated vendor.
The Camburg and RPG lowers I posted are Raptor spec (factory Raptor width), you would need a Raptor spec upper to match. Alpha1 (Outlaw Raptor brand), ICON, Camburg and RPG all make Raptor spec uppers - my two favorites are the Alpha1 and ICON billet uppers but the tubular UNI's are good pieces also and much less expensive. I would have preferred the Alpha's but the uni wasn't sealed like on the ICONS and I live where they salt the roads...
You are correct - Raptor spec width limits you to RPG and Camburg (SDHQ also sells the Camburg lower but don't confuse it with their in house LT kit).
A UNI UCA typically gains our trucks about 1.5" of droop travel - meaning extra down travel, no impact on up travel. However, your UCA won't work with a Raptor spec lower.
technically (just so you understand) it's more than the difference between 2.5 and 3.0 - it's also a 8" stroke vs 10" stroke - they are physically longer as well as larger in diameter.
Honestly, if you aren't out in the dirt every weekend pushing the limits of your truck, you will probably never know the difference. Is there a difference, yes - does it matter for the vast majority of guys, no.
I beat the **** out of my Raptor so I went with max capability while staying within stock parameters - 14" of travel up front with dual 3.0s, 16" of travel out back with a 2.5" bump kit while retaining 100% of the bed functionality. My truck still retains 100% of it's factory utility (full disclosure, I chose to ditch the hitch but I could have kept it) yet is 10 fold more capable. You have to decide what your threshold is for 'performance' vs utility. You can turn your truck into a prerunner but then it's just about worthless for anything else.
LT shackles will lower the truck about an inch but will add that inch back in droop travel. In terms of 'leveling', you should have the ability to adjust your coilovers up or down for the ride/height you desire.
I have a Deaver +3 pack with a LT shackle - so yes, I would recommend it
You can absolutely swap out the 2.5 for 3.0s without changing anything OR you can run the 2.5s. Remember, the shocks control the deceleration of the suspension (hence the name, they control the 'shock' of suspension movement from an obstacle) - ergo a larger unit will outperform a smaller unit - if you run with an empty bed, the 2.5s are probably ok until you start running harder. LOTs of Raptor guys just add deavers or nationals and an RPG bump kit and leave the factory Raptor shocks on the rear. Believe it or not, some keep the fronts but swap in a heavier spring from Eibach and rave about the results - still not as good as a 3.0 but much better than factory.
This pretty much points to something like the Dirt King setup so you can increase your capability but retain the front coilovers you currently have. IIRC TAP Auto indicated that there is a 'modification' used to run the 8" stroke coilovers with the Dirt King kit - that 'should' mean that if you decide to upgrade to a 10" stroke 3.0 at a later date, you could remove the spacer or whatever its and bam! I'd call the guys at Dirt King and verify before I spent the money (like do they have a kit for your year group, able to use 10" stroke coilovers, etc...).
Hope this helps.