It will indeed be cheaper to do everything as a bundle pack. If I could have afforded to I would have. I have a 5-speed with RA gears in it already, so didn't want to wait another 2-3 months to save up for a 6-speed with it too. However going to keep my "emergency" fund with enough for a 6-speed swap if it ever comes down to that. Hopefully won't though, and not really expecting it too.
However, taking a loan out to do car upgrades? IMO not exactly the smartest move... I'd take out as little as you need to get the job done if the car is down and NEEDS to be back and running ASAP.