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Indy bushings have definitely changed a lot over the years, both stock and aftermarket sets, but the main differences, as already noted, the older ones were both taller (especially the tops) and harder, their old catalogs still show this too. I have some of each, but it is easier to just post images that are already online right now.
There have been three main variants of the aftermarket bushings that I know of, the first being the small clear bagged hang sell versions, which came in three options, red, orange and black, all conical shaped and so much harder than now.
* Just measured and the tops were almost 12 mm tall, bottoms 13 to 14 mm on some sets, but I used to cut the red tops down for Stage 9 trucks and they worked really well - still have some in trucks and on boards from that time.
Red 92 duro (not so soft but softened up nicely over time)
Orange 94 duro (fairly hard and remained hard)
Black 96 duro (rock hard and never really broke in)

Then there were the white boxes, which were way more "normal" but some sets still had taller tops, maybe old stock, others pretty much similar to what they are now, which might have been the revised sizing. They also included the low bushing line - just a lower top bushing, same bottom bushing, also in three options, red, orange and black. Some packaging had the red as 90 and others as 92, some had orange as 92 and others as 94 and the black ones were still 96 from what I can recall and what I have here.
Red 90 / 92 (a fair bit softer than what they were before)
Orange 92 / 94
Black 96 (still rock hard)

Lastly the newer clear plastic containers, five bushing options, same as they are now, also still had the low top option for a while, conical in red, orange, blue and black, cylinder in all - white 78, red 88, orange 90, blue 92, black 94, yellow 96. All of these bushing options were way softer than any of the older ones, with a few funny things, like the red ones being a more solid feel but still squashed down a lot, the orange feeling more soft than the red and softer than the stock orange and a few other things.
The newer bushings felt like the break in time was way less and I could have a set running really well after one session on mini ramp, compared to maybe a few sessions on older bushings. They also seem like they hold up really well overall, minimal issues with them blowing out or any other problems, although I have seen almost every brand of bushing destroyed at some point, but maybe more so the tops being cut from the washer than anything else.
As to the exact timeline of them, I don't know right now, but I thought I had noted it down somewhere at some point, but I had the old clear bag through stage 9 so up until maybe 2009 / 2010, then maybe the white box from stage 10 through 11 and then the expanded options in the clear plastic boxes from around 2015 or so.
I think more than anything, they were just easier to get than most others but I have picked up a lot more of the old bushing packs from shops closing and "found stock" that have been sold off every now and then.