Guys thanks for the suggestions. newbieinkc, to answer your main question is the manual correct? Yeah, for the most part the manual is correct. At least for the strobes (its possible that the return lines aren't) as I tested the continuity between the switches in the manual on one strobe, and they were fine.
But, I got everything working. First of all, how did I test this? I put it into switch test mode. And depressed the switches by hand. The six I mentioned didn't work, in that they didn't show up on the display. After posting this, I decided to try it in a game setting. One reason this is different is that in switch test mode you need to depress the switch for several seconds (that is the game only tells you want switch is depressed like one a second or two) So I went into game mode, and the switches seemed to behave better (in contrast, a couple of weeks ago, the switches weren't working in game mode, and so I bought some capacitors. )
Anyways, the H only seemed to work if I held it down, while the other two (A and M) worked if I just quickly depressed the switch. The H originally had a capacitor, but I removed it. I had read elsewhere you should only have capacitors on the roll overs and other momentarily depressed switches. But since this switch seemed to work if I held it down, I decided to put a capacitor back on it.
While I had the playfield out, I decided to go ahead and replace the capacitors on the drop targets. These are hard to get to, which is why I skipped it earlier.
Finally I cleaned the switches on all the roll overs (as well as the H, A, and M) I probably should clean the outlanes as well.
Between replacing ALL of the capacitors, and cleaning the switches (and making sure the switches make contact when the rollover/trigger is depressed) I think I got everything working!