I just saw it today, I figured it out last week

I hope you saw my post saying that was a possibility before you spent too much time

Turns out the ignition module plug and the plug on the throttle body were reversed. Thanks for the help

Those were the only codes, checked twice. I disconnected the harness again and moved out of the way as if the engine was being removed again looking for any wires that weren't connected or damaged wiring but didn't find anything. Beginning to think a broken wire somewhere

ok, these codes have to do with the throttle body sensor which has nothing to do with the ignition spark.
651 - maximum govern speed override
652 - fuel rev limit
both of these codes are related to each other and happen if the engine over rev's for more than 0.150 sec. When it detects this condition the MIL light will turn on during this condition.

Are you sure that was all the codes?
generally if the ecm is bad it will display a code for that, if there are no other codes it has to be something you did when you reconnected the harness's or something. If it ran before you R&R'd the flexplate i'd say it was something you disconnected during that process or something related.

Figured out which pins are A and D. Reading two codes 651 and 652

I don't have a diagnostic jumper, can't find anything that tells me which pins are A and D

Don't know what year you have so I don't know if this applies to yours. The ignition module connector is the exact same as the heater mounted under the throttle body. The harness is long enough to switch them around accidentally. I went on a service call about a month ago that gave me a real headache thinking the wiring diagram was wrong. They replaced the rear main seal. And when they reinstalled the motor they switched connectors. They also smoked the module doing that, so if you discover that's what you've got, don't be surprised if it still doesn't start.

the switch by the distributor is the actual oil pressure sensor, the one by the oil filter is for the light on the dash so if the pressure drops too much it will turn on the light. The one by the distributor actually disables the ignition if pressure is lost.
as for the wrench light flashing on the dash? It may just be telling you there is a problem and to do a diagnostic by jumping out the diagnostic plug on terminals A and D. (it is a square or oblong 4 terminal black plug, located either by the ecm or on the wire harness somewhere back in the engine compartment). On smaller trucks it is under the floor plate on the RH side.

Using a Diagnostic Jumper to Diagnose the ECI System
If you do not have access to a laptop computer, it is still possible to access the diagnostic trouble codes stored in the memory of the Spectrum system ECM using a diagnostic jumper and the malfunction indicator lamp. With the key OFF, connect the diagnostic jumper to the DLC located near the ECM. The jumper will connect diagnostic pins A and D. Turn the ignition ON but do not start the vehicle. The malfunction indicator lamp (MIL) will begin to ?ash.
The MIL displays three digit codes by flashing the first digit, pausing, then flashing the second digit, pausing, and then flashing the third digit. There will be a long pause between codes. For example, a code 143 would be one flash followed by four flashes followed by three flashes.
The MIL will first display a 166 three times. Code 166 indicates that the ECM based diagnostic routines are functioning. Then, any Diagnostic Trouble Codes stored in memory will display three times each. The MIL will then start over with the code 166. If the vehicle is started while the diagnostic jumper is in place, the MIL will flash rapidly.
Diagnostic Trouble Codes may be cleared from the system ECM memory by moving the ignition key to the OFF position and removing the (F2) system battery fuse for at least 15 seconds.
NOTE: This will erase all of the memory in the computer including the adaptive learn.
Follow this and you will get the codes.
There are too many codes to list here so just get them and i can tell you what they mean.

The ground strap is connected, everything seems to power up when key is on. This particular engine has a oil pressure switch by the distributor and a oil pressure sender by the oil filter. I have continuity through the switch when cranking the engine but no continuity through the sender. The wrench light flashes on and off with key on but doesn't seem to be any code

first i'm going to assume this is a GM vortec 4.3L? I'm sure it is :o)

one of the first things i would verify is if you have the ground connected right.
there is a negative cable from the battery that connects to the frame/engine but there should also be a second ground strap aside from the battery cable to insure a good ground. Usually connected from the starter mount bolt to the frame.(it actually may not be on the starter mount bolt but it should be from the engine block to the frame) But generally if you turn the ignition on and the system powers on, dash lights up then your ground should be good and your problem is in the ignition circuit somewhere.

secondly, check the dash MIL light (it may be a specfic light on the display or it could be the neutral light flashing if it has one) see if it is flashing a code.
since you've already replaced the usual suspects check the main ignition fuse.

also check the oil pressure sensor, it too can cause a no spark scenario. (it's mounted right beside the distributor).
good luck
:o)