yes and I use it on both sides of a 4' wide strip of 3/4" MDF. For shims I use a pack of cedar shingles from Menards adn sift through them to find the super-thin ones or sand them down. If you use a flat enough table, you should be able to shim the joint only at the point where a pin won't self-hold after inserted. On a 75g sump build I did, I only needed 6 shims on a 9' seams. My test on those is that after i get them all snug, if I can blow the joint with canned air and not move any pins, I'm good.
I don't push the shims in after pulling the pins. IMO this is not necessary. Think about it. If you get the joint all lined up and pins in and they're all nice and snug, then you pull them and push in the shims more to "snug them up" then you have no frame of reference to tell which shims are not snug enough, which would leave an area or weaker pressure that you would not be able to 'see'. Plus shims are angled to you would tend to push up on the bottom piece of acrylic more in one area. So don't touch the shims after you're done pinning, just pull the pins and you're good.
Then I run the solvent, scoop bubbles if there are any, pull the pins, check for drift, and throw some weight on it. My fav weight is 12 packs of pop LOL.
I don't use EDC because of cost. It allows for longer soak time (or working time for long joints) without causing crazing IIRC.
Are your edges prepped with a router? Do you make sure all the 'pits' are trimmed off?
I'm thinking if you re-snug the shims significantly, this might be what's going on.