Bubbling secondary after weeks

I followed the brew instructions 100%, it was in the primary for 5 days, moved to secondary (glass carboy) and after 13 days it started to bubble again...whats going on? One day it did get kinda warm...like high 70's

Atmospheric pressure or temperature changes will often cause co2 to be released from solution.

So I slowly cooled it back down, and it does seem to still be bubbling. I was supposed to bottle them today. Should I wait till it stops? Should I start taking gravity readings?

Definitely wait until it stops - more precisely, wait until fermentation stops. Yes, check gravity, and then wait three or so days and check it again. If it's stable, then bottle. Ignore the bubbling - it really doesn't tell you anything. The only way to know if it's done is to use the gravity readings.

Sometimes the instructions are useful, more often than not, they're crap. Sounds like the instructions that came with your kit are not so good. Just ignore the timing schedule in the instructions. THe beer is ready when it's ready, not when the instructions say.
Cheers!

Really at 13 days it should probably still be in primary. In the future, take gravity readings to determine that you are at final gravity before transferring to secondary (if you do a secondary at all - you will have to read up on skipping the secondary).

In this case I would wait another few days then take a gravity reading, wait another 2 days and take a second reading. If they are the same it is safe to bottle it.

Also read up on fermentation temperature control. Controlling the temperature of the fermentation is probably the most important place to concentrate in order to improve the taste of your beer.