I'm at about the same stage you are with my conversion, using almost the same parts, LS3 crate etc. My car however is a 68 Lemans that is being converted to a GTO.
I ordered my wiring harness and computers from Speartech since for one reason or other I didn't like the other aftermarket solutions. The GMPP harness requires special software to tune and is not compatible with OBD2 scanners. It also does not talk to an auto transmission controller. The cost of this solution with a GMPP transmission controller is about nearly $2000.
Mast Motor Sports makes a harness/computer that looks very good on the surface but is not truly OBD2 compatible, supports only VDO CAN gauge and cannot be scanned by an OBD2 scanner. By the time you add the transmission controller you are at nearly $3000.
Speartech make a harness and uses GM computers for both the engine and transmission for $1695. This was the choice I made since it can use any of the standard OBD2 scanners, gauges or tuning software. The Speartech solution will also give you cruse control it you want it, which the other two do not. (Mast tells me the cruse has not been done on their computer and is not a high priority).
The main point of interest here is that your selection of a 4L60E will depend on what controller you use. Speartech tells me that for a 4L60E to work with the LS3 and factory GM controllers (NOT GMPP) that the transmission will have to be configured like it is being installed in a 06 Trailblazer SS and not like the typical Camaro transmission that is commonly used. Apparently the output shaft and control electronics are different.
I also had sticker shock when pricing starters.

I have not purchased mine yet.