Not sure what year your engine is, but if it's a 289, you will need a flexplate that has a 28.5 oz imbalance for your 4R70W. Your stock C4 shifter and linkage will work fine, without the need for cables. You may need some exhaust work, because the new transmission is a little wider than your old C4.
You will need a special crossmember for this swap. The bolt holes are all basically the same, but the transmission's bolts are about 2" rearward from your C4's mount, if I recall correctly.
Other than the possibility of needing your driveshaft shortened (which may not be the case!), you shouldn't run into anything weird. =)
Yes my engine is the original 289. Its good to hear that the stock linkage will work. according to this guys "how to" if I change the tailshaft I can get a new shorter driveshaft compared to shortening mine.
now when you mentioned the flexplate this guy used a 50oz 164 tooth flexplate for a 1990 mustang 5.0 AOD.
The part that really sucks is everyone says you cant run tri-y headers and I have one year old ceramic tri-y's
Here is the parts list he has on his how to. if you see anything that seems odd or unnecessary let me know. Thanks Grim.
Ebay:
-2001 Mustang V6 4r70w WITH speedo splines on the output shaft
-AOD tailshaft RF-F2TP-7A040-AA
-450 lb Low Lift Transmission Jack 7 1/4" to 23 1/4" Lift Height Inc Strap Cradle
CJ Pony Parts:
-AOD Transmission crossmember TRA-656-639
-AOD Transmission starter index plate TSP12
-AOD Inspection plate INSP10
-T5/AOD Conversion 50.5" driveshaft DS5
-T5 28 spline Driveshaft yoke T5Y
-65-73 Transmission Mount TM2253
Late Model Restoration:
-AOD Torque converter nuts HDW-377704S
-AOD transmission to engine block bolts HDW-6392B
-AOD flexplate to crank bolts LRS-6379AK
-4r70w trans fluid/filter/gasket LRS-4R70WSVC
Summit Racing:
-B&M Transmission cooler 70268
-Headman shorty headers 88400
-Lokar shift boot 70-FMB
Baumann Electronic Controls:
-Quick 4 Electronic Transmission Control System
LKQ Dismantlers OKC:
-2001 V6 Mustang automatic shifter with cable
-1995 Mustang automatic shift nob
Amazon:
-Jones Exhaust Sxp4 2-1/2stamped X-Pipe
-Derale 13017 Transmission/Engine Oil Hose for the trans fluid to cooler lines
-Heatshield Products (204012) 1/2" ID x 10' Hot Rod Sleeve Roll to shield the trans lines