Quoted from markronz:

I did read your posts. My pins did not have corrosion on them. The pins simply would not come out, and I did verify that I did buy the right tool. A tool which cost me $11 something for a tiny piece of metal. After removing 3 pins in 20 minutes and cursing up a storm, on my 4th pin removal I broke my tool. So last night I did order the molex connectors (granted I had to buy 22 port ones instead of the 21 port ones). Coincidentally the most of the molex connectors with shipping was $11. So if the end game is to get the wires out and cut the connectors off anyway, then I would have just been further ahead to go get the new connectors as a whole, cut the wires outright and avoid myself some frustration. I should have just did that instead of buying the tool. Same cost, same result, less headaches.
I get that in the long run, had I already owned the removal tool, that using it would save me money in the future down the road, if it worked and i was able to use it multiple times. But I'm not sure that I will have more than one pinball machine. So owning this specialized tool, which is now broke anyway, does nothing for me.
Don't get me wrong I appreciate the help. And I don't doubt the authenticity of your procedure you listed, the fact is it wasn't working for me. So maybe like someone else said, you're just more skilled that us at the removal.
So with all that said, the only thing left up in the air, which I won't know until my GPE order arrives, is if the 22 pin connector is a suitable replacement for the 21 pin one. If someone has any idea, I'd love to know. Or if you know where I can purchase a new 21 pin connector, I'd love to know that too. I couldn't find them anywhere. Otherwise if the 22 pin one does not work, and I can't find a 21 pin connector, then I will probably go buy an eyeglass screwdriver tool for 99 cents and suffer through removing the pins from just those 21 pin connectors. I'm not going to buy another $11 tool that I will just break again.

Quoted from markronz:

Ok I see my mistake now. In Clay's System 1 repair guide it says:
"Molex card edge pin extraction tool, part# 11-03-0003 or 11-03-0016."
So from Mouser electronics, I bought the 11-03-0003 part here:
http://www.mouser.com/ProductDetail/Molex/11-03-0003/?qs=sGAEpiMZZMv%252bZqqdCpW8N8I58JeN4OGt
That is $11 but it does not come with the rubber butt end piece. I found that strange, now I know why. So I had to fashion my own end for it.
If I look up 11-03-0016 on Mouser, I see it here for $15:
http://www.mouser.com/ProductDetail/Molex/11-03-0016/?qs=%2fha2pyFaduilNHMC564LRe0JDDNn1FI1pb4EIEuG%2f6g%3d
So I guess I should have really ordered one of each. I know there's two sized pins according to the repair guide, so that other part, the 0003, must be for that other pin. I guess the wording on Clay's repair guide, what with the use of the word "OR" made me think that it meant OR. Foolish me. So I guess I did have the wrong part after all then.
Regardless, if I need one or both of those tools, they cost $11 or $15 respectively, not including shipping. All new molex connectors cost me $11 and I think that included shipping. So I still stand by my original statement that if you don't intend on repinning multiple different machines or anything, it still makes sense just to buy all new molex connectors. Especially since you said the 22 pin one should work. Either way I have to cut the original connector pin off. So why spend money on an expensive removal tool which can (and did) break when you could just buy new molex and save your self some arthritic pain. Granted the removal surely would be easier with the right tool. But that doesn't change my point about the prices.
Anyway just my two cents. Looking forward to the new molex arriving, thanks Ed. Thanks everyone else too for the help.

Quoted from markronz:

I bought other things from mouser, so that's why I bought that tool from them initially. But, that is besides the point. My point is, I don't need the removal tool because I bought all new molex connectors. So I can just cut all the wires and easily re-wire stuff into the new molex. No need for the tool at all. Had I know this originally, I wouldn't have bought the tool to begin with. i would have just bought all new connectors and been done with it.