I have had dealings with all of the companies below with the exception of fordpartsdiscounted.com and my experiences with them were problem free. Some of the parts may be able to be found cheaper elsewhere, or may be substituted with other brands or stock parts to save money, but this should give you a solid starting point as to what you need to buy and some places to buy the parts. There may be some small odds and ends that still need to be found, but to the best of my memory this list is complete.
http://www.ultrarev.com
Fidanza Aluminum Flywheel - PN#: 186501 - $319.00
http://www.buyfordmotorsport.com
King Cobra Clutch (Disc, Pressure Plate, Throwout Bearing)- PN#: 7560-C302 - $169.00
http://www.steeda.com
Steeda Tri-Ax Shifter - PN#: 555-7353 - $179.95
Steeda Clutch Adjuster Kit (Quadrant, Cable, Firewall Adjuster) - PN#: 555-7042 - $99.95
http://www.summitracing.com
ARP High Performance Series Flywheel Bolt Kit - PN#: ARP-100-2801 - $7.88
ARP Pressure Plate Bolts - PN#: ARP-150-2201 - $7.95
Energy
Suspension Transmission Mount - PN#: ENS-4-1104R - $26.95
http://www.stangparts.com
94-95 V8 T5 Transmission - $750.00
94-95 T5 5.0L Bellhousing - $200.00
86-01 Shifter Bolts - $25.00
86-95 Bellhousing Bolts - $25.00
86-95 Transmission Bolts - $25.00
86-95 5.0L 5spd. Flex Plate - $44.95
94-95 5spd. Pedal Assembly - $175.00
79-99 Leather Cobra Shift Knob - $35.00
http://www.50resto.com
1979-04 Lower Shifter Boot - PN#: LRS-7277 - $36.95
1994-98 5-Speed Shifter Boot & Bezel - PN#: LRS-04567CAA - $194.95
94-95 T-5 Steel Bearing Retainer (Transmission may include this already, check first!) - $48.95
http://www.fordpartsdiscounted.com
94-95 Pilot Bearing - $14.42
94-03 Release Fork - $26.76
Other necessary parts:
T4M0 5spd. EEC (Necessary for perfect driveability)
Manual Transmission Harness
Dust Cover for the bellhousing to cover the clutch cable and fork
Total - $2412.66 (Almost exactly what i paid for my complete swap with all stock parts from ampperformance.com)
If you have any other questions about anything, feel free to drop me a PM.