Weird bumps on balloon molly

[c_long20]

I've had this Molly for about 6 months. I got her for free because she has one eye. She was pregnant then and had her little fishy about a month later. 55 gallon tall tank with led lighting and fluval u4 filter. Water tests were nearly perfect.
There some bumps on her fin and body. She also swells sometimes and her find stick out a little, but only for a day or so. Seems to be swimming and eating just fine. Any suggestions?

 

[Rbishop]

"Nearly perfect" isn't very definitive for us. Exact readings from a good liquid test kit?

 

[c_long20]

Gh-12, kh-11, chlorine-0
Ph-7.0, am-.25, no2-0, no3-0

 

[c_long20]

Still have this issue. Seems to be getting much worse. Some help would be appreciated. Added 2 new pictures.

 

[myswtsins]

Not very experienced with fish illness...At first it looked like tumors but now, I have no idea. Do you still have ammonia readings? I hope someone with more experience with illnesses comes along.