True, the tunes do more for the trans shift strategy, which does make a very nice improvement in how the trucks run down the road, especially under high loads like seen while towing heavy. But they also make the most of the engine output within the capacity of the stock injectors and timing curves, I see a noticeable performance increase between my 87 and 89 Octane Performance tunes, nothing huge but it's there under the skinny pedal when needed.
As far as 5Star realizing that the trans is the key upgrade, I don't think they sell any gear upgrade packages. . They, as a TUNING company seem to focus on the tunes and items that directly impact the tunes, like intakes and headers. I think downstream items like gears are outside their wheelhouse as a tuning company, that shouldn't be taken as meaning that a nice tighter shift strategy (with no additional trans gears or ratio changes) is superior to improved final drive ratios. I've got both (plus good headers) and the gears were hands down a bigger performance increase than the tunes (which are very nice), no question about it.
I don't see how a stronger and tighter trans rebuild that doesn't add any new gears or change any internal ratios can bring that additional performance, better drive ability sure but where exactly is the performance gains coming from? But hey, you seem convinced that a well built TC and trans are the hot ticket to better performance, so go ahead and prove me wrong. . I have another five years of heavy towing in front of me with my EX and may need to deal with the trans at some point, so I do look forward to seeing what you can do with yours.

A chip? They still sell chips for these? What you want is a tuner like Coop said above, and 5Stat Tuning (site sponsor and the go-to guys for 6.8 custom tunes) will write a set OD custom tunes for how you use your rig. However with yours being a stick you won't get the best part of the tunes, far better Auto trans shift strategy, but you will get the better engine response and the little bit of engine output the tunes supply.
As has been said many times before (by most here.....) GEARS are the single biggest performance improvement you can do for your V-10, what are you running now?