So thought I would update this post with the issue and fix for my problem (since I hate finding posts where the author doesn't include the fix). As all the members who posted before stated, the bearings were the issue. I will post some pictures of the transmission after I pulled it out, you can see the bearing in the casing is completely missing (shredded apart) most likely causing the shafts to not be balanced with 1st and 2nd gear.

You can see the shaft isn't straight with the other one and bearing is completely missing

New bearing in the housing while old bearing is right below it

Here is the transmission put back together with all new bearings and synchro's with the rebuild kit that zcardepot provides. The shafts rotate smoothly now with the gears compared to when I removed the transmission. Needless to say, can't believe I drove the car for almost two years like this and even a day at autocross. I would baby 1st and 2nd gear trying to stay out of those gears during the years I drove the car so maybe that helped but however I am shocked I still have a transmission and no other damage was done. Thanks to everyone for the help. I can gladly pound through all gears now with confidence.

It is surprising they will function in that condition. There are pretty tough overall