Engine lights keep coming on saying engine systems failure and transmission malfuntion but car still drives normal

the overdrive light flashing on a A4Od transmission is a fault signal for the transmission , just like a ck engine light but for the transmission only , get a code read to find the fault stored in the ecm and then you'll know what exactly it is
its very common for engine swaps to have a few intermittent sensor failures on restart due to the connectors all getting maybe not all the care and protection they deserve in the swap (plastic baggies) and having a bit of dirt and corrosion in them now (spray contact cleaner)

with the od in/out/in/out an educated guess is that the engine throttle position sensor is not being read now , but a code reader will tell all

Ok what about transmission codes most obd2 readers wont read trans codes or its a short in the computer

I would say you check for codes & then diagnose the
system they point to

A strong suspect is a vacuum leak in the system.
If it is an emissions related leak the engine light will also come on.
The power brakes can also be affected by a leak.

With the engine light on, it stores a failure code. If you take the car to a mechanic he can use a code reader to determine where the failure is ocurring, helping to isolate where the leak might be. They typically have a few tricks for finding vac leaks.

If you are a do it yourselfer, you can borrow a code reader at Schucks to reveal the failure as well. Then the work begins to troubleshoot and track down the leak, most often a cracked hose.

Good luck.

look 214 is not a valid code for a 1995 escort, this is an OBD1 system. here is a list of trouble codes for this year of ford no matter the model.

You should find the diagnostic connector under your hood normally by the fender on the battery side. By just using your test light and a jumper wire, it will tell you what kind of problem you got.

KEY ON ENGINE OFF (KOEO) TEST
Model years 1984-1995 all models of Ford
1. Make sure engine is fully warmed. If in doubt, run engine at 2000 rpm for 2 minutes.
2. Turn ignition off and wait 10 seconds for system to shut off. Make sure A/C is off and transmission is in Park (automatic) or Neutral (manual).
3. Hook up light and jumper (or a tester if you have one). Turn key to ON (do not start engine). Read the codes.

How to do it?

Example code 23: your test light should flash 2 long consecutive flashes followed by 3 short pulses.

Ford's common codes for OBD1 (vehicles made before 1995)

11 system pass
12 idle control fault
13 dc motor did not move
14 engine rpm signal fault or PIP circuit failure
15 eec processor or power to KAM interrupted
16 rpm to low to check oxygen sensor test or fuel control error
17 cfi fuel control system fault or rich/lean condition indicated
18 ignition diagnostic monitor (IDM) circuit failure
19 cylinder identification (CID) sensor input failure
21 engine coolant temperature (ECT) out of self-test range
22 manifold absolute pressure (MAP) sensor circuit out of range
23 throttle positioner sensor out of self-test range
24 air charge temperature (ACT) sensor out of self-test range
25 knock not sensed during dynamic response test
26 transmission fluid temperature out of self-test range
28 loss of primary tach, right side
29 insufficient input from vehicle speed sensor
31 egr positioner sensor below minimum voltage
32 egr positioner sensor below closed limit
33 throttle positioner sensor noisy/harsh on line
34 egr valve circuit out of self-test range
35 egr valve circuit above maximum voltage
38 idle track switch circuit open
39 axod torque converter or bypass clutch not applying properly
41 oxygen sensor circuit indicates system always lean
42 oxygen sensor circuit indicates system always rich
43 oxygen sensor out of self-test range
44 air injection control system failure
45 coil 1 primary circuit failure
46 coil primary circuit failure
47 4X4 switch is closed or oxygen sensor failure
48 coil primary circuit failure
49 electronic transmission shift error
51 engine coolant temperature sensor circuit open
52 power steering pressure switch circuit open
53 throttle position circuit above maximum voltage
54 air charge temperature circuit open
55 key power input to processor open circuit
56 mass air flow circuit above maximum voltage
57 axod circuit failure
58 idle tracking switch circuit fault
59 automatic transmission shift error
61 engine coolant temperature circuit grounded
62 converter clutch error
63 throttle positioner circuit below minimum voltage
64 air charge temperature circuit grounded
65 charging system over voltage
66 mass air flow sensor circuit below minimum voltage
67 neutral/drive switch circuit open
68 transmission fluid temperature over temperature range
69 transmission shift error
70 data circuit communication link circuit failure
71 message center circuit circuit failure
72 insufficient manifold absolute pressure (MAP) change during dynamic response test
73 insufficient throttle positioner (TPS) change during dynamic response test
74 brake on/off (BOO) circuit open
75 brake on/off (BOO) circuit closed
76 insufficient air flow output change during test
77 brief wide open throttle not sensed during test
78 power interrupt detected
79 a/c on/defrost on during self test
81 map has not changed normally
82 super charger bypass circuit failure
83 OIC-low speed fuel pump relay circuit failure
84 egr vacuum regulator (EVR) circuit failure
85 canister purge circuit failure
86 shift solenoid circuit failure
87 fuel pump circuit failure
88 electro drive fan circuit failure
89 transmission solenoid circuit failure
91 no oxygen sensor switching detected
92 shift solenoid circuit failure
93 throttle positioner sensor input low
94 torque converter clutch solenoid circuit failure
95 fuel pump secondary circuit failure
96 fuel pump secondary circuit failure
97 transmission indicator circuit failure
98 electronic pressure control circuit failure
99 eec has not learned to control idle

engine runs smooth if giving more than idle pressure. It is when the motor is engaged with transmission at start the engine lopes and wants to cut off. If I press the throttle hard it takes right off. If I come to a stop I can put transmission in neutral to keep it from cutting off. This creates a shifting that is not normal and I'm afraid it is a sign of failure coming.

I have a code book and in the generic section it says transmission control system malfuntion. that might not be it but you could start checking that area.

The SERVICE light coming on, indicates a fault detected by the vehicles on board computer. The fault might be transmission related, or possibly engine/emission related. Push the OFF and WARM buttons TOGETHER on the climate control panel ( with the ignition key on ) Hold for 5 seconds and failure codes should appear . Relay your findings. Hope this helps

Lexus's have a complicated system of electronics that control the function of the transmission.Under normal operating conditions the transmission is controlled by the ecu and by a secondary system called a drivetrain control module. usually when a fault occurs it sends a code to the ecu and the check engine light comes on.
If this light does not come on then typically the electronic modulator is at fault and needs to be replaced.
If the check engine light comes on when the vehicle is hot i need this code to guide u further for the repair.
If u want to attempt the repair , be wary. its messy and takes time to do to do it right.

its an egr CIRCUIT MALFUNCTION which means can be any type of problem with the whole circuit -- wiring --connections fuses relays etc not just the egr valve more than likely the valve was good need to check and test the whole egr system