One side it did decent job, the other side not so much.

I tried 3-4 passes, scrubbed it in, let it sit, and nothing to get some patches out.

I still have some bad spots as shown in the picture, so wondering what my next step should be. Muriatic acid next? i know that stuff is POWERFUL, so trying not to go that harsh, but maybe i have too. Only other consideration was using a "gel-based" oxalic acid cleaner. Starbrite has some and FSR is gel based. 

You can spray it on with a spray bottle or pour some in a small container and put it on with a sponge type applicator. There's no real reason to use it above the water line.

Don't buy the more environmentally friendly version of muriatic acid. Go to a hardware store and ask for the nastiest stuff they have

The Transchem brand stuff in the link below works really well.

http://www.acehardware.com/departments/home-and-decor/cleaning-and-disinfectants/specialty-cleaners/12787?store=17471&gad_source=1&gclid=Cj0KCQjwu8uyBhC6ARIsAKwBGpQOFt6h66g2F4QQaDpEh41l4jLb3ATjFQ_0iRFmhNJB-dNqTN9F6qUaAtZ5EALw_wcB&gclsrc=aw.ds" rel="nofollow - link

And here's a link to an old thread on hull cleaning with muriatic acid.

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=43148&title=cleaning-hull-help" rel="nofollow - link

PS............you could probably get answers to the other related questions you asked on Planetnautique, but you should ask them here first 

been holding off on muriatic acid because i'll need to wax after...  but i finally think i know what to do, and am going to order orbital buffer, pads, compounds, polish/wax to do this on a weekend.

I'm no expert but it seems to be going the buffer, compounds route before cleaning is kind of backwards and going to end up kind of a mess.  I'd give a good cleaner one more shot.  This question comes up a lot on boating forums.  There are always 100s of great answers, a few of which might actually work.  You got the household cleaner (like CLR) crowd.  Forget it, not close to strong enough.  You have the tidy bowl crowd, I dont know, maybe.  The hardware store acid crowd, sounds like the route you went, again, maybe.  Then there is the specially made boat cleaner crowd...like me.  I like Mary Kate On and Off Gel.   Not a chemist, so I dont know the difference, but hydrocloric + oxalic + phosphoric) Unlike all the light liquids that splatter and splash and dont stick, the gel sticks to the side of the boar (and the bottom, ugh, but I do it every fall).  Let is sit for about 10 minutes, hose it/wipe it off.  Stays in the water from April until Oct/Nov every year and by the time I put it away, it still looks new. 

https://ibb.co/kHNN9cf" rel="nofollow">

It's possible, it may be a long weekend depending on things that don't show up in the picture.

Don't be afraid of the muriatic acid, put it on the stains from the waterline down and you won't have to worry about whether or not it affects the paint. 

Edit......the stuff Larry mentions works good too It has hydrochloric acid as one ingredient. Muriatic acid is watered down hydrochloric acid. 70% water, 30 % hydrochloric acid. Mary Kate on off 65 % water, 35 % mix of 3 acids.  Pick your poison  In the first post it says he used Starbright instant hull cleaner (specialty boat stuff) it's not nearly as nasty or effective as the on-off or the muriatic acid

If the sides were stained, what's the bottom of the boat look like.....probably not too good at all.

I'm not sure what your thinking is with the acid and wax. Do the acid, then use all those things that you're ordering

Whatever you end up deciding to do, the last step will be to wax the thing anyways