I used to suffer similarly on rides over about 25 miles. I found that some padded cyclewear caused more discomfort than others (but had discomfort to some degree with all) - based on how wide and thick the padding was in the affected area - some pads just seemed to get in the way/rub me up the wrong way more than others. I also found that the sweatier the pad got, the worse the problem got - dampness was a major factor. I switched to roubaix tights (Tudor Sports York tights) with no underwear or padding, or thin silky microfibre trunk style underwear with a bit of length in the leg beyond the crotch (regular M&S type stuff - not cycling specific) with Endura Hummvee cycling trousers. This improved things a lot but still didn't fully resolve the issue.
A friend gave me a Selle Italia Epoca leather saddle and the problem has disappeared for me. I'm not sure what the saddle has contributed to the fix but I suspect a big part of it is that the leather is a lot "slippier" and so there is less friction against moving surfaces. I also suspect there is some improvement in my "sitting" position/saddle shape, also causing less friction. I can't remember the last time I cycled more than 40 miles in one go and so I can only vouch for this up to about that distance.
One other thing - if I've been off the bike for several days (weeks), I can get a little sore first ride out. Also, if you do get sore, I would recommend that, if possible, you keep off the bike especially for longer rides, until the affected area has healed.