Well I went ahead and tried the metal chain trick with evaporust, soaked the tank for a full day and put it on its side, upside down, etc. to remove the rust. Seems like it had done a fairly good job! And it took out a lot of gross scaling. 
Dried out the tank with a gallon of acetone and I also used that as the "wash" to remove the scaling and big pieces of rust. I had a fine woven hand cloth as a filter on top of a funnel so I'd empty it from the tank, back into it's container, then back into the tank. I did that like 7 times. After I left it dry over night, I checked it the next morning by shaking it to see if I head anything else and not really. 


 This was the only area I found surface rust on, but seemed really light so I'm not concerned about it.

Here's what came out of it. 




My set up.
Friday, I poured in the liner. I am still waiting for it to cure, Caswell says anywhere from 3 - 5 days for cure time, so I am going to wait a while before I see if my job was a success. Overall, it was pretty straightforward. My only worry is that there are bubbles that formed in the surface of the liner, which none of them seemed to have popped, but I'm worried this might lead to delamination or something. Not sure if that's just how it applies and maybe is normal.
While I've been waiting, I got the bike to start up almost instantly Saturday morning. My tach cable was not attached correctly so I couldn't see idle speed but it was definitely high. I took it down my driveway anyways and down the block for some testing. At some point, about halfway through my test ride, it start to bog with throttle and then it died which was weird. So I started walking it back and letting it cool, then once I got to a downhill area I started it back up and got to ride it the rest of the way home. I'm not sure if that was just a fluke or what. Then, I put my left engine cover back on and accidentally crimped my oil pressure wire, so I looked down during the second test ride and saw that my oil light came on, freaked out, but saw no trail or oil and smelt nothing so I just took it back home quickly and checked. That was a silly mistake but an easy fix. The last thing I did was go to synch the carbs, for some reason #3 would not adjust at all, regardless if the set screw was in or not, so I have to take a look at the linkage and see if it needs adjustment. However one of the videos I was watching online said Honda considered them within spec if they were half an inch off. So perhaps this is no big deal for now. 
The highest gear I could get it in was 3rd, I think the fastest I went was about 40 yesterday. I have a feeling that 4th and 5th are just not engaged correctly which is frustrating, but for one season I can live with just backroad gears. I don't know if maybe I have to be at a higher rpm and speed to get the bike into those gears but I'm doubtful it's anything like that. If anything, I'm just impressed I somehow messed that up even though I followed a video and have 1, neutral, 2 and 3 perfect. Lol.
Next on the list is likely new spark plugs so I can keep testing, new throttle cables, and a new gas tank seal. I bought shorty throttle cables from 4into1 and for some reason I can't get the cables to stay on the carb end. Coming down from throttle one of them always disconnects because there's too much slack. But I have them set up like OE spec where they cross over onto the left side of the frame. So I'm unsure if I should buy shorty ones again or buy OE and have really long cables but maybe they'll have less play in them.