Has baby been evaluated for lower labial (lip) tie? This can affect his ability to maintain good suction and latch really deeply (the clicking makes me wonder. . .). Upper labial may also be an issue, although there isn't consensus about how much of a difference a tight upper frenulum makes.
I also wonder about oversupply, based on your comments about compressing, sore nipples, and high weight gain in a baby with a poor latch. Is baby possibly compressing to slow flow? Coming off the breast when you have a let-down? Other signs of oversupply (http://www.llli.org/FAQ/oversupply.html)? If this is an issue, working to resolve it will probably help significantly.
I agree that seeking a Occupational Therapist w/ lactation experience (not all have any!) is another good idea. An OT can help you with finger exercises to help baby with correct latch. There are finger exercises to help with tongue extension (some babies with frenulum issues need to learn new tongue positioning after clipping) and with bubble palates. Quote from Lisa Marasco on Dr. Brian Palmer's website: “A “bubble” palate is a high spot, often the size of a finger indentation, that has a back rim. It may extend width-wise from gum line to gum line (wide bubble), or be a smaller indentation in the middle. As you feel the infant palate, your finger will go up, come down the back side or “wall”, and then have to go “around and past” that wall to reach the juncture of the soft palate. Your pad-side up finger loses contact with some of the hard palate in order to reach the soft palate. Babies often gag when you go past the bubble because they are not comfortable with it, even though it is normal to draw the breast back to that juncture, usually about 1.25-1.5” deep. Babies with bubble palates tend to rearrange themselves on the breast into a shallow latch, and I use pacifying on a properly placed finger to help de-sensitize them to deeper placement, sneaking back slowly.”
Also, treating the thrush is important. The steps you listed (garlic, GSE, probiotics, vinegar) are helpful but are unlikely to resolve already established thrush on their own. Lots of resources for treatment on the LLLI website, kellymom.com, or Jack Newman's site. Remember that all 3 of you (both nursings!) need to be treated simultaneously, which might mean hunting for a knowledgeable doc if you use prescription meds. I'd actually think Newman's All Purpose Nipple Ointment would be a good choice if you have sore nipples from latch issues and from thrush, as it will treat both issues (http://www.nbci.ca/index.php?option=com_content&view=article&id=76:all-purpose-nipple-ointment-apno&catid=5:information&Itemid=17).
Good luck, Mama. You're doing a great job. It sounds like you've had a really rough postpartum with this new baby. I think sometimes when we're nursing older children, we forget how hard and frustrating nursing a newborn can be. It WILL get better, and your months/years of nursing when it's easy will overshadow the difficulties.