Before you try to remove the bypass line and install your trans cooler kit, access to the top of the transaxle will be much better if you remove the cap screw on either end of the air box, then pry up on it at the ends and it will pop out of its mountings. Move the air box out of the way. Secondly, you will see a black painted plate held to the passenger side of the trans case with three bolts. This holds the shift linkage cable. Remove the three bolts and move the assembly aside. Note: you do NOT have to remove or disturb the cable. Now you have good access to the two fittings at either end of the "line to nowhere" at the top of the transaxle. Buy or borrow an open end AN fitting wrench for 1" fittings from Summit Racing or similar supplier. They are under $20 bucks and as they are quite short, will allow you to swing it in the tight confines you will be working within. These are also aluminum and anodized so you will be less likely to mar the new aluminum AN fittings that come with the kit.
Take your time and the entire job shouldn't be more than 2 hours the first time you install one. Probably half that time once you've previously done one.
Good luck. usmcfred