I am 3/4 of the way into a 2nd floor hardwood install. So far I have laid the flooring perpendicular to the floor joist as recomended (joist run top to bottom hardwood left to right). I have come to the last room over the garage and after removing the carpet I see the floor joist are running left to right. I have doubled checked the run of the joists on the 2nd floor and and this room is the only one were the joists run opposite to the rest of the 2nd floor.

My question is....do I continue laying the hardwood left to right to match the rest of the 2nd floor (it's just a bedroom so not a high traffic area) as it would be more aesthetically pleasing, or do I run the hardwood top to bottom, across the joists, but it would look weird as this room would be the only one opposite to the rest of the second floor?

A couple of things. It is common to change direction at doorways with wood flooring. It's done all the time. But if you must have the flooring going the same direction, then go into the garage and attach blocking between the flooring joists. Use 2 x 6's every 16". You can off set every other one to enable you to nail through the joists and into the ends of each block using # 16 sinkers. Add some subfloor adhesive to the tops of each block and over cut them by 1/16" to pressure fit them into place. Use dry lumber, not soaking wet stuff. You will not be able to swing a hammer between those joists bays. So a framing nailer is ideal, or a screw gun. It's a PITA once the subfloor is down. If you cannot get to it from below, you could consider removing the subflooring, installing the blocking, then re-installing the subfloor.

We installed blocking. Piece of cake as long as you can get to the joists from underneath.

One thing to consider:

Some framing nailers are too big! Too big to fit easily between the joists that is.

I wound up buying a palm nailer, $45 at Menards, and using that. A wonderful device the palm nailer is.