So I recently had my top redone and used all new pump, lines, cylinders and etc. Initially it worked great, then after the second or third time I lowered/ raised it it didn't go all the way back up. Taking a look in the trunk I saw that there was no filler plug in the reservoir and everything in my trunk had now turned pink (everything on the floor that is, there was no pink on the bottom of my well liner and no fluid anywhere I could see above pump height). I did find the plug in the trunk so I assumed that while filling and priming the guys who did the install overlooked putting it in. I refilled the pump and ran the top up and down to get the air out of the lines, then I put the plug back in. Drove the car to a friend's put the top down, everything is fine. Went to put the top back up last night and it did the almost close again. Looked in the trunk and the plug had popped out and there was atf on the floor again. The lines do not leak and the plug is pretty hard to get in and out, so it would take some force to pop it out. Any ideas? I'm going to call the top place in Florida where I bought my parts sometime in the next day or two, but I thought I'd ask here in the mean time.

The only thing I can think of is the pump is over full and creating undue pressure. Make sure the pump is filled to below the fill hole.

It is below the fill hole, I filled it when it was level. I think the manual says fill to within 1/4" of the bottom of the hole.
What if the lines were to be put on the wrong sides of the pump front to back? Would that make a difference in anything other than which way to push the switch in my dash?

Once its bleed and full the level in the res should stay consistent because as the cylinders are moving in any direction and fluid is entering one side its exiting the other side.The one thing that comes to mind is a bad seal in one of your cylinders or a bad pump aerating the fluid causing the fluid to expand and blow the fill plug out.A wood splitter is basically the same thing and mine was doing what I just described because the seals in the cylinder were allowing fluid to bypass heating and aerating the fluid causing it to blow out the vent also resulting in massive pressure loss.

I called hydro-e-lectric and he said if there is any air in the line it could cause it. As the air in the line moves into the reservoir it stays there and builds up. He said it might not have been bled all the way initially and then filled while the top of the car was up. It is certainly conceivable that I myself did not get all the air out, as the seats are in the car and I cannot see most of the lines. In the next couple days I'll try again, cycling it open and closed several (instead of one or two) times and then fill while the top is down. The guy on the phone didn't act like it was the end of the world so hopefully it's no big deal. Fantastic customer service by the way.