Boniness of the butt and a bit of discomfort there probably means at least that you are using your sitbones (isicheal tuberosities) to sit on. That is a good starting point.

I have found that finding the right pad and bike shorts is an experiment in brands until your find the right one. It is a bit like hunting down the best saddle for you.

The chamois pad in shorts does come in various dimensions, and unfortunately, there is no consistency in them. You might find a pair that has the right spread for your sit bones, but is way too wide through the perineum area and up the front so they bunch and chafe. And you might find a pair that feels right through that region, but misses your sitbones, so they get a beating.

My favourite brand is Pearl Izumi, too, and I reserve them for long rides. I found a much cheaper range (torpedo7, a New Zealand company) that has similar dimensioned padding for training and touring and general stuff.

However, before my hiatus from extended riding, I was getting into the habit of riding with just flat-seamed running or compression shorts that are similar to bike shorts but without the padding. Admitted, my sitbone areas were well conditioned, and I have Brooks B17 saddles on the bikes. I went with just plain underwear on a ride this past Saturday for around 15km and suffered no ill effects (so I must be getting back to full conditioning of my butt!).

I agree that gel is not OK if you are intent on doing longer distances. It tends to compress the flesh in your butt, causing issues with nerves (numbness) and circulation. A harder, thinner saddle with flex built into the shell is more conducive to comfort.

Anyway, measure up the pad of the shorts that suit you now, maybe add a bit more to the area under your sitbones, then have a look through the ranges at various bike shops until you find the ones that match. I know it seems a bit odd taking a tape measure in or a template, and measuring up shorts like that, but it sure can help before you get to the try-on stage to eliminate the ones that aren't suitable.

One other short-term solution until your boney bits become more conditioned is to wear a second pair of padded (or maybe unpadded) shorts over the top of your current pair.