You have to make sure you are putting in an electronically compatible transmission with the current wiring harness meaning if the car has an auto then you need to use a 98 auto. If you are switching to a manual then you need a manual harness.
The 4.2L engine is not a direct drop in for a 1998. The 99+ cars can pretty much do a direct swap as long as you are using the correct balancer and flywheel.
For a 98 there are fuel rail differences and sensor differences along with other small things that will need addressing.
List everything you have and you would probably get a better answer than just telling us you have some parts and want to know what works. Unless you are very mechanically inclined, this is not an easy swap.
Early 97-98 4.2s had a 2-pc main girdle that connected the 1st to the 2nd main cap and the 3rd to the 4th main cap and had larger main bolts. Mid-1998 and up 4.2s used a 1-pc girdle that only connected the rear 3 main caps and had smaller main bolts.
To use the early 4.2 in any
Mustang will require replacing the girdle with a newer 3 main style from a 4.2, a 99-up 3.8 girdle or just delete it. You will also have to cut the girdle studs sticking out of the head of the main bolts on the 1st main bearing. The 99-00 3.8s used a factory windage tray/girdle that is better than nothing but certainly not ideal. The 01-up 3.8s use the same windage tray/girdle as the 4.2.
Late 00 3.8s are actually early 01 spec engines that are internally balanced. If you have one of these.....just use the notes for an 01-up.
Here's some extra info. 97-98 4.2L engine are directly compatible with 94-98 3.8 crank pulleys. So if you have a 97-98 4.2 crank and balancer, you can use your 3.8 crank pulley/underdrive pulley.
94-98 Single port heads
- 4.2 shortblock
- Single port heads/fuel rail/intake
- Mustang 3.8 water pump
- Auto
trans = 4.2 or 01-up flexplate
- 5spd = 01-up or rebalanced 3.8 (0 or neutral) flywheel and a pilot bearing
- V6 Mustang bellhousing
- Re-use your stock cam position sensor
- 01-up 3.8 oil pan
- 01-up 3.8 oil pick-up tube and screen
- 4.2 damper or 01-up 3.8 damper (use the 01 pulley for blower cars)
- Re-use the stock 3.8 oil pressure sender and tube
- Re-use the Mustang headers
- You can use the 4.2 or 3.8 dipstick. Just keep track of where 5 qts puts the mark when refilling with oil.
94-98 Split port heads
*** You will need to perform all the mods required for a split port conversion plus these steps for the 4.2 ***
- 4.2 shortblock or longblock
- You can use the 4.2 heads
- Mustang upper and lower intake
- Custom return style fuel rail (VMP has them)
- Mustang 3.8 water pump
- Auto
trans = 4.2 or 01-up flexplate
- 5spd = 01-up or rebalanced 3.8 (0 or neutral) flywheel and a pilot bearing
- V6 Mustang bellhousing
- Re-use your stock cam position sensor
- 01-up 3.8 oil pan
- 01-up 3.8 oil pick-up tube and screen
- 4.2 damper or 01-up 3.8 damper (use the 01 pulley for blower cars)
- Re-use the stock 3.8 oil pressure sender and tube
- Re-use the Mustang headers
- You can use the 4.2 or 3.8 dipstick. Just keep track of where 5 qts puts the mark when refilling with oil.
99-00 split port heads
- 4.2 shortblock or longblock
- You can use the 4.2 heads
- Mustang upper and lower intake and fuel rail
- Mustang 3.8 water pump
- Auto
trans = 4.2 or 01-up flexplate
- 5spd = 01-up or rebalanced 3.8 (0 or neutral) flywheel and a pilot bearing
- V6 Mustang bellhousing
- Re-use your stock cam position sensor
- 01-up 3.8 oil pan
- 01-up 3.8 oil pick-up tube and screen
- 4.2 damper or 01-up 3.8 damper (use the 01 pulley for blower cars)
- Re-use the stock 3.8 oil pressure sender and tube
- Re-use the Mustang headers
- You can use the 4.2 or 3.8 dipstick. Just keep track of where 5 qts puts the mark when refilling with oil.
01-up split port heads
- 4.2 shortblock or longblock
- You can use the 4.2 heads
- Mustang upper and lower intake and fuel rail
- Mustang 3.8 water pump
- Auto
trans = your stock flexplate
- 5spd = your stock flywheel and a pilot bearing
- V6 Mustang bellhousing
- Re-use your stock cam position sensor
- Your 01-up 3.8 oil pan
- Your 01-up 3.8 oil pick-up tube and screen
- Your stock 01-up 3.8 damper
- Re-use the stock 3.8 oil pressure sender and tube
- Re-use the Mustang headers
- You can use the 4.2 or 3.8 dipstick. Just keep track of where 5 qts puts the mark when refilling with oil.
3.8tranny on a 4.2 engine 
