Maybe you should just be working longer at the weights you're doing under 100lbs. Your body needs time to adjust to lifting, especially with an exercise as complex as the squat. I'm training my brother right now; he's been at it for about a month and a half and is still squatting 95lbs, but his technique is fairly solid and he's making good strength gains.
I don't know much about the 20-rep squat program; i haven't looked much into it because I've got more than enough mass as it is already, lol. If you put on 20lbs over the course of the routine, you obviously did something right, but maybe some research before any next attempt at a weightlifting routine would do some good. I just updated the sticky topic on fitness-related reading material (finally), check out Starting Strengh above anything else. When I read it I realized that my routine had a few crucial opportunities for improvement and my results benefited very nicely.
If you're going to start lifting again I'm not sure whether it'd be a good idea to vary your stance too much; starting out you're really supposed to get the basic lifts down before you change it up too much. Work more on the weights you're comfortable with now and move up from there. You say that you're more bodyweight-oriented now, though; maybe you'll want to stick with those exercises. I'm sure you've seen trainforstrength.com spammed across the gamefaqs message board countless times by now; can't really go wrong with that routine..if you can stomach it, it used to kick my ass.
I do a full body strength-training workout three days a week. Squat, bench, and row on Monday. Squat, deadlift, and standing overhead press on Wednesday. Then Squat, bench, and row again on Friday. The days vary depending on my ability to get myself to the gym

Where I am with weight now is (5RM followed by ORM):
Squat: 355lbs 405lbs
Bench: 205lbs 245lbs
Deadlift: 315lbs 385lbs
Standing Overhead Press: 185lbs 205lbs
Can probably do more on the overhead press, but it's a dangerous lift so I haven't pushed it.