So for now im going to put back that original hot, and maybe buy some more caps. Should i post a pic of my chassis to see what exact model it is?
Posting some detailed pics of your chassis would be good to identifying the exact revision. IIRC there are at least 5 variants (maybe more) of the MS9-29 and it's possible that the cap list is different between them.
MS9-29A (Astro chassis variant with manual degauss)
MS9-29N (Namco maybe?)
MS9-29T (Taito chassis variant with auto degauss)
MS9-29S (I don't know where this one was used)
MS9-29SU (Sega Universal chassis variant, designed for Hitachi tube, found in Twin units and other Sega machines)
Now that I have done this, what would be the best thing to do now. Should I go through each one and double check polarity plus uf matching? Is there a list I could reference? I was using 300wins list after the fact, before I knew that these kits would vary.
There's a cap list on AO:
http://wiki.arcadeotaku.com/w/Nanao_MS-9_capacitor_listing
there's a cap list here:
http://www.juniorsrevenge.com/nanaoms929caplist.txt
I'm sure there are other lists floating around online too.
If this were mine I'd make a spreadsheet, in the first column put the cap location number, in the second column put the farad and voltage as specified on your cap kit list, then in columns 2,3, etc list out the caps specified in any of the online lists you've found. Finally look at each cap you installed on your board and mark the farad and voltage in it's own column also check the polarity of the cap against the polarity on the silkscreen (note that the silkscreen marks the positive pin while the cap casing marks the negative pin) ...
Do you still have the old caps? if so try to figure out which cap went to which location and mark down the value in it's own column on the spreadsheet
highlight any row where any differences exist... ESPECIALLY if the farad rating is different or if your new cap has a lower voltage rating than any of the other columns.
I've not done done an MS9 cap kit but it seems as though the pi-polar cap can indeed keep it from running if a suitable replacement is not used:
http://forum.arcadeotaku.com/viewtopic.php?t=19053
If your new cap is not by polar then re-install your old one in that spot. Same goes for any location where there is a mis-match (wrong farad rating to voltage to low).
I would do all this first and check over all the boards for cold joints or damaged traces, re-flow as needed. test before swapping back the HOT. if the above fails to revive the board then replace the HOT with the old one and be sure to reinstall the plastic isolation shield if it had one and use non-conductive thermal paste.
Also wheres the best place to buy caps?
Depending on your chassis you don't have much choice unless you build your own. I've bought from Ian Kellog, from Arcade Buffett, From Arcade Cup, from Twisted Quarter, Syracuse Semiconductors. They all use high quality caps and include decent documentation. The only place I wont order cap kits from again is Bob Roberts only because the few kits I've ordered from him used cheap low-quality caps.
As I said I've never had a kit that matched 100%. the best kits will only have a few caps with higher voltages than the originals, which should be fine, mistakes are made sometimes so if anything beyond that is off I'd rather skip that cap, document it and move on. Replacing it with the wrong value cap can cause more problems. In most cases there are only a handful of caps in high-stress areas that are problematic but it would take more time to test each and every one (to properly test a cap it needs to be removed anyway) so it just makes more sense to replace them all. but if anything is out of the ordinary you're better off sticking with the original cap so long as it's not visibly bloated or leaking (in which case you should order a proper replacement if one was not included with your kit).
EDIT:
I should note most places that sell cap kits have never actually attempted to use their own cap kits. They buy capacitors in bulk and and then build the kits from cap lists online or from the chassis schematics. Which is fine, but that's a big part of the reason you can't 100% trust anything but the old caps that are already installed din your monitor.