Thanks man. I'm just going to deal with the gap and check it everytime I have my car jacked up.
I have a bigger problem though. The new bolt holes don't line up with my diff flange. The new DS bolt pattern has slightly more space between the bolt holes then my old one, so I can get 2 bolts in on the same side but I can't get the other 2 bolts in, because the DS holes and diff holes don't line up. So we called the place I bought the driveshaft and they're claiming that it doesn't make sense, and that for a '75 280Z coupe the driveshaft should fit. Also the bolt holes themselves are larger than on the old DS. I can wiggle the bolts around if I slide them in. I don't see why datsun would change the distance between the holes for no reason. Maybe a Z expert can chime in on that.
So now I need to find out what year diff I have I guess? Did certain years of S30 differentials have different bolt patterns on the flange? It's possible my diff and driveshaft were switched out at some point in it's life, but I don't know what year it was switched with.
Also the new driveshaft is half an inch shorter than my old one, but it doesn't make much of a difference.
I'll go take measurements of my old DS bolt pattern to help find out what kind of diff this is. Then I'll edit them in this post.
Edit: I measured the distance between the bolts diagnolly from the center of the holes and got 2.75". I also found this pic of differential flanges, mine is exactly like the left one. While I was doing this my dad got a call from the driveshaft shop and they said they found a flange with the same pattern as mine, and are going to custom make me one today to fit my diff flange. So hopefully everything works out and we don't have to do this a second time.
Edit2: I just found out that I might have an R200 diff. I found comparison pictures between an R180 and an R200 and the cover on mine looks just like the R200. So that explains why the driveshaft shop had such trouble. Also, I don't think it's an LSD. With the car jacked up if I spin one wheel the other wheel turns the opposite way.
Edit3: I'm only updating this still because I think this info will help people that might get in a similar situation. A lot of this seems obvious by now.
I found out that from 70-78 S30s all use that differential flange on the left. Except '75 S30s, they use the middle flange. When I ordered my new driveshaft I told them my car was a 1975 280Z manual coupe, and that was that. Never occured to me that my diff might've been swapped. So they shipped me a driveshaft meant for that 75 Z flange. Since my car has an R200 from some other Z/ZX it didn't fit, and here we are now. I'll get my new driveshaft with the proper bolt pattern soon and then everything will be fine.
Here's where I found the pic and the info on S30 diff flanges. http://jagsthatrun.com/Pages/Parts_DAT_driveshaft_flange.html