Thanks for all the feedback! I'll address your questions in order.
The pack originally was a 50L Jam in size medium and it had the compression system you described.
The webbing loops on the sides are modifications to the original compression system - so they're made from the same webbing that came stock on the pack.
So far I've been rolling the top closure similarly to how you've rolled the one on your pack. (Your pack looks wonderful by the way.) I secure it by tying a bit of cord through the loops on front and back of the roll-top area or the pack - essentially identical to the original mechanism, except with cord and knots instead of straps. I have to admit I didn't think through the decision to cut the straps from this area of the pack, but I don't really mind tying the pack closed instead of buckling it.
I made the modifications to the Jam in stages. I would trim a bit and make sure I was comfortable with the change. After a while I would trim some more. Eventually I ended up with an almost completely bare-bones Jam. It would have been wiser for me to plan all of the modifications first instead of working through a process perhaps best described as "creeping elegance" - taking steps without any vision for the end product.
I've recently switched from a thin foam sleeping pad to an Exped Synmat UL 7. Before, I would roll my pad up, insert it into the pack, and let it unroll to serve as a structured shell for the pack. Then I would put a trash compactor bag inside and fill it with the rest of my gear. I haven't gone on a trip with the new pad yet (although I'm very excited to.)
I haven't settled on "the best" way to pack considering the new pad yet. I'm currently considering two options. For one, I cut a portion of the old foam pad which fits in the back area of the pack (adds 1.75 oz.) I think this might give enough structure to somewhat mimic the way I packed before. The other option is to do what I did before, except with the new pad. I'm not sure which is better, or if a combination of the two makes a difference. Maybe you have some advice here.
I love the idea of using 3/32" cord instead of bungee cord. I'm definitely going to make that adjustment. I tried a compression system similar to the one on your pack, but I used bungee cord and I needed loops on the sides closer to the bottom of the pack. I'm now planning on adding such loops and using rigid cording instead of bungee cords.
Here's a picture to clarify what I'm describing. It's very similar to your pack.
(The black lines are arrows from text to their described elements. I point that out because they aren't very good arrows and might appear confusing...)
I appreciate the input and especially the constructive questions. Thanks!
*edited to add the picture