My 2001 with a 3.9 has 220 K on it and runs like crap so I did a compression check and all cylinders are between 70 and 90 psi so I bought a motor with 120 K on it to swap. Now my question is about the distributor, this new motor has had it removed and I don't know how to line the new one up when I put it in aside from the rotor pointing toward #1 plug wire when at TDC.

 

This is from the 2001 FSM.

INSTALLATION - 3.9L/5.2L/5.9L
If engine has been cranked while distributor is removed, establish the relationship between distributor shaft and number one piston position as follows:
Rotate crankshaft in a clockwise direction, asviewed from front, until number one cylinder piston is at top of compression stroke (compression should be felt on finger with number one spark plug removed). Then continue to slowly rotate engine clockwise until indicating mark is aligned to 0 degree (TDC) mark on timing chain cover.

(1) Clean top of cylinder block for a good seal between distributor base and block.
(2) Lightly oil the rubber o-ring seal on the distributor housing.
(3) Install rotor to distributor shaft.
(4) Position distributor into engine to its original position. Engage tongue of distributor shaft with slot in distributor oil pump drive gear. Position rotor to the number one spark plug cable position.
(5) Install distributor holddown clamp and clamp bolt. Do not tighten bolt at this time.
(6) Rotate the distributor housing until rotor is aligned to CYL. NO. 1 alignment mark on the camshaft position sensor.
(7) Tighten clamp holddown bolt to 22.5 N·m (200 in. lbs.) torque.
(8) Connect camshaft position sensor wiring harness to main engine harness.
(9) Install distributor cap. Tighten mounting screws.
(10) Refer to the following, Checking Distributor Position.

Checking Distributor Position
To verify correct distributor rotational position, the DRB scan tool must be used.
WARNING: WHEN PERFORMING THE FOLLOWING TEST, THE ENGINE WILL BE RUNNING. BE CAREFUL NOT TO STAND IN LINE WITH THE FAN BLADES OR FAN BELT. DO NOT WEAR LOOSE CLOTHING.
(1) Connect DRB scan tool to data link connector. The data link connector is located in passenger compartment, below and to left of steering column.
(2) Gain access to SET SYNC screen on DRB.
(3) Follow directions on DRB screen and start engine. Bring to operating temperature (engine must be in “closed loop” mode).
(4) With engine running at idle speed, the words IN RANGE should appear on screen along with 0°. This indicates correct distributor position.
(5) If a plus (+) or a minus (-) is displayed next to degree number, and/or the degree displayed is not zero, loosen but do not remove distributor holddown clamp bolt. Rotate distributor until IN RANGE appears on screen. Continue to rotate distributor until achieving as close to 0° as possible. After adjustment, tighten clamp bolt to 22.5 N·m (200 in.lbs.) torque. The degree scale on SET SYNC screen of DRB is referring to fuel synchronization only. It is not referring to ignition timing. Because of this, do not attempt to adjust ignition timing using this method. Rotating distributor will have no effect on ignition timing. All ignition timing values are controlled by Powertrain Control Module (PCM). After testing, install air cleaner assembly.

 

You may of done the compression check wrong or it was a bad tester I know I had that happen to me got bad results and was thinking of a new engine but decided to retest and on second test I was in great shape turned out the first tester had a missing seal. There is a way to test if it’s either the heads or the piston rings if it’s the heads get the heads redone much simpler than swapping out engines.

220K is a lot of miles though so you may be right.

Can’t help with the distributor sorry

Did you look at the free service manual on this forum it may tell you that bit of info on the distributor alignment.