Poping noise when braking

Hey guys, I have an 06 Prius that I have had for about a year or more now. When I bought it, it needed a transaxle. I replaced that and have been driving it since. I have this problem that seems to be getting worse. When I push the brakes the car will make a popping noise, and it seems to be getting more frequent. I do not get any noticeable noises when turning or just driving normally. The noise is quite noticeable, when I am in a parking lot and hit the brakes next to someone, people will give me the look like "what's wrong with your car". I am not positive where this noise is coming from, but my best guess is that it is coming from the right side. The popping seems like something is bound up and then releasing. I can also replicate the noise some times when I initially accelerate. My best guess is that it is being caused from the engine/trans weight shifting, but I am not sure a motor mount can make the popping noise I am getting. Any help?

 

Also, something worth mentioning is that the popping that I experience is usually in the middle of me slowing down, not the initial push of the brake pedal. For example I can be going 60mph and I start to slow down to a stop and while applying even braking pressure to the pedal the pop will occur around 30 mph. Prius are new to me and I don't really understand how our regerenitave braking works, but I am wondering if this has something to do with that. Not sure is something is releasing at the point I get the popping noise.

 

anyone?

 

I jacked the car up in the air last night and the springs and struts seemed fine, so I started looking around at everything else. I was hitting things with a rubber mallet and prying on things with a pry bar. Since my subframe had been taken out while I did the trans swap I checked all of those bolts. The only bolts that were not really tight were the two 14mm (hex head) that hold the rear of the lower motor mount, mount to the sub frame. I was able to turn each of those ~ a full turn. I also unbolted the lower engine mount to look at that, and the mount looked fine, but with that mount removed the engine really will move a ton front to back. Is that the only mount that is on the car that cushions the front to back movement? After an hour or so of poking around and not really finding much other than what I just listed I put the car back on the ground. I drove it into work today and I did not experience popping yet....so we will see. I want to give it a little more time before I claim victory.