Hi Mike,
I found the Rubber Magic makes a big difference. At first I thought it might be a gimmick but if you have not tried that I suggest you give it a try. I witnessed it with mine, and initially was very hard to close, took a good slam and sat even higher than yours does but it settled down real quick after using rubber magic. After spraying it and leaving the boot shut for the night the seal has actually compressed on the corners, and this morning was much easier to close. I will take a pic when I get a chance.
In regards to the front 1/4 vent seals I fitted mine just before Christmas and they fitted well. The holes are not punched for the pivot points, and I had to cut a fair bit out. I used an old one as an example but mine went in okay once I compared matched it to an original one.
Also I have fitted my rear quarter window seals, and they fitted well. Yes it does take a bit more force to clamp and latch the rear windows as it seals really well, but not that bad. I haven't given them a spray with rubber magic but will do them too. As they are out of the box I am able to latch shut and open my pop out windows okay.