Has the balance shaft delete and timing belt(recently) been done or does it need addressed while out?
I did mine on a budget (purchase whole v6 5 speed and used the dvz tranny) works for me because i only road trip to the coast a few times a year in it, i usually use my excursion for road trips. My passat is my dd for work which is all back road or city driving. Some may never notice a difference in rpms, others do. Mpgs a minimal sacrifice. I can buy lots of diesel for 700 bucks at 35 to 42 mpgs
Parts car that had new axles $400(parted and scraped out so i ended up breaking even)
BS delete with timing belt/water pump kit $500
Stage 2 tune with 5 speed tune and imob delte
With egr delete: $500 iirc
Whitbread 35 lbs sm flywheel with fx300 clutch: $1500
Fresh oil, coolant and filters $125
Labor: free but cost me a weekend and some evenings
Optional items to consider
New thermostat and housing : 100
New coolant T: 50
New tandem pump gasket: 20
Imported proper tdi geared tranny from Franz: 700
As far as labor goes i can only give an estimate i run an outdoor power equipment shop and other than the owners vehicles and his landscape company vehicles i only do power equipment with occasional atvs and golf carts
I'd probably charge labor on swap only about 1200 or so for just a 5 speed swap and about 1500 to 1700 with the bs delete and new timing belt with the other common service items that are easiest addressed with motor out.
I dont do work on the side because my own crap keeps me busy and i find that when people want you to do side jobs they want to pay side rates. If i do a side job i charge more than shop rates because my off work time is worth more to me than at work time. There are more than a few very reputable shop owners on here that can give a better idea labor cost than i can. Labor in NYC/LA will cost you more than West Virginia or Detroit. Just as i can buy a 4000 sq ft new home here for what i can buy a 1958 single wide trailer with hurricane damage in the keys.
Keep in mine this is just spit ball estimates and based on what i paid nearly a year ago so prices in my memory bank may be fuzzy and could increase/decrease.
Hope this helps