I'am a first time floor layer and finisher floor went down great sanding went great but the finish not so good. I used Bona natural stain and then put 2 coats of Traffic down with a t-bar. I have what looks like raised grain and a couple of thick spots where I missed with the t-bar. So I have a few questions on how to fix it.
1. what to use to smooth out the finish
2. How long should I wait before I do it.

Any other helpful hints would be great. Thanks in advance

You will need to buff (abrade) the floors to get them as smooth as possible. If you don't know how to operate a circular buffer, rent a square buffer. Use a 220 sanding screen to thoroughly abrade and smooth the floors. Hand sand edges and corners with 220 sandpaper. Repair missed spots be reapplying finish in the missed area, feathering it out as well as possible. Vacuum up all dust and tack with a water dampened clean towel till NO dust remains. Apply a final coat. Don't miss areas and don't get puddles. Harder to repair than to do it right the first time. You don't have to wait at all. Once dry, the finish can be buffed and coated.

I wanted to put three coats on so I have 2 on now after hitting it with 220 would you put one more coat on or two. Also isn't the finish too soft to sand right now would it be better to wait a couple of day to cure more. Last question what are the problems with using a circular buffer verses a square buffer. I take it they are hard to get good results with so the square one is easier for the novice.

The square buffer is way easier for a novice. I suggest that. As for waiting for the Traffic finish to cure, it is 75% cured in three days, as long as you mixed in the hardener. Bona recommends buffing after 48 hours for increase adhesion and provide a smoother finish. When I use Traffic, I always apply three coats and buff lightly between each coat. Three coats of Traffic at 500 sq.ft. per gallon per coat is a lot of finish and should provide many years of protection.

Ok this may be a dumb question but it has been 48 hours today can I wait another couple days to buff and apply another coat or even till this weekend or should I go rent one tonight and get it done. Also thanks for all the help.

It doesn't matter. Buff and coat it when you have the time. Think of it as a "re-coat".

Thanks for all the help. My neighbors are doing a hardwood floor too and they are putting down tan oak what color putty would you use, red oak or white oak.

i make my own using putty and artists oil paints.
i use cadmium orange, cadmium yellow and burnt umber. using those 3 should match most woods easily.