I like poly, but some others don't. I prefer to use the PST polygraphite stuff and and not had issues with squeaks. I also have not had any issues with ill fitting lower control arms with them. I have heard of others using Energy or Prothane have have had some fitment or squeaking issues. The fitting on the lower control arm is a function of the strut rod bushing, so make sure everything lines up correctly before locking down the torque.
I'd also agree with using the offset upper bushings instead of poly in the upper arms. The offset will allow you a greater range of caster adjustment, provided you install them the opposite of the instructions. You can substitute the adjustable strut rods to gain a bit of caster, but, when you use these to offset the location of the lower control arm, you can put it in a bind at greater travel. With proper install of the bushings, you don't "need" an adjustable strut rod, but it may help a bit
Personally wouldn't worry too much about going with 11/16 tie rods. The 9/16 units can withstand 5gs worth of loading before failure, so they really don't flex much at all.
Biggest improvement you can make for both ride and handling is good shocks. Not gas charged parts store units, not KYBs, but a good high end shock. Like tire technology, shocks have improved tremendously over the last decade, never mind 20-40 year old stuff. If you're sticking with the stock t-bars with plans to step up in teh future, this will help a lot.
Since you have the stock sway bars, upgrade to a 1.125 solid or 1.25 hollow front bar. These improve lateral stability significantly while turning. The stock front unit you have is pretty wimpy comapred to whats on the market today. The rear isn't so bad, but the adjustability of modern units is nice. Maybe down the road you can upgrade to one of those.
Alignment will be the final piece of the puzzle. Radial tire tolerate a wider range of angles before they show unusual wear, which allows more aggressive settings. Once your machine is all back together, set the ride height you want and instruct the shop not to change it, then request positive caster of 3-5*, negative camber of .5-1* and total toe in of .125 to .1875 of an inch.
You didn't mention it, but if you don't have them now, the addition of subframe connectors actually benefits the suspension greatly. Reducing flex in the vehicle better allows the suspension to do its job without wasted energy. For that matter, the radiator core support bracing and inner fender supports also provide big gains in rigidity.
