Mazda 2001 626 Idle problem

If I understand you correctly, the problems started after you remove and clean the intake manifold is that correct? If it is most likely you have a vacuum leak and the intake manifold causing one or two dead cylinder, recheck your work.

Is the engine light on?

Idle Air Control (IAC) Valve
IAC valve is an electromechanical device controlled by the PCM. The IAC valve is mounted on throttle body and allows air to by-pass the throttle plate. The amount of air allowed to by-pass the throttle plate is determined by the PCM and is controlled by a duty signal.
During cold engine operation, the IAC valve opens, raising fast idle speed to a predetermined RPM. The IAC valve also compensates for all engine loads during warm engine operation to maintain a preset idle RPM.

IDLE CONTROL SYSTEM
SYSTEM CHECK - MPV
Ensure engine is at ambient temperature. Connect scan tool. Using PID/DATA monitor and record function, select ECT, IAC V and RPM PIDs. Start engine.
Engine speed should decrease as engine reaches operating temperature. If idle speed decreases, go to next step. If engine speed does not decrease, check ECT sensor, IAC valve and wiring.
Allow engine to warm to operating temperature. Check for DTC P0506, P0507 and P1504. If no DTCs are present, go to next step. If any DTCs are present, diagnose and repair as necessary.
Using scan tool, select SIMULATION TEST. Change duty value of IAC valve to 100 percent. If idle speed increases, go to next step. If idle speed does not increase, check IAC valve passages and wiring.
Using scan tool PID/DATA monitor and record function, select A/C SW, ALTF, IAC V, PSP SW, RPM and RPM DES PIDs. Ensure idle speed stays in specification when accessories are operated. See IDLE SPECIFICATIONS table. If idle speed is okay, check is complete. If idle speed is not okay, check suspect component and circuit.

IDLE SPECIFICATIONS
Condition(1) Idle Speed
No Load700-800
All Accessories On (2) 700-800
Power Steering Operating700-800
A/C On800-900
(1)In Neutral or Park.
(2)Headlights, fan switch is in position "3" or "4", cooling fan and rear defroster are on.

BY-PASS AIR CONTROL (BAC) VALVE (MILLENIA)
On Millenia 2.3L, BAC valve is located on rear of front cylinder head. See Fig. 35. On Millenia 2.5L, BAC valve is located underneath throttle body. See Fig. 36.
On all models, ensure engine is cold. Start engine and let it idle. Idle speed should gradually decrease as engine reaches normal operating temperature. If idle speed does not decrease, check coolant hose to BAC valve. Repair as necessary. If coolant hose is okay, replace BAC valve.
Fig. 35: Identifying BAC Valve (Millenia 2.3L)
Courtesy of MAZDA MOTORS CORP.
Fig. 36: Identifying BAC Valve (Millenia 2.5L)
Courtesy of MAZDA MOTORS CORP.
IDLE AIR CONTROL (IAC) VALVE
Miata, MPV, Protege & 626
Disconnect IAC valve connector. Using an ohmmeter, measure resistance between IAC valve terminals. See IAC VALVE RESISTANCE SPECIFICATIONS table. If resistance is not within specification, replace IAC valve.
Millenia
IAC valve is part of By-Pass Control (BAC) valve. Disconnect IAC valve connector. Using an ohmmeter, measure resistance between IAC valve terminals. See IAC VALVE RESISTANCE SPECIFICATIONS table. If resistance is not as specified, replace BAC valve.

IAC VALVE RESISTANCE SPECIFICATIONS
ApplicationOhms
Miata, Millenia 2.5L, MPV & 626 2.5L(1) 8.7-10.5
Millenia 2.3L(2) 10.7-12.3
Protege & 626 2.0L(3) 7.7-9.3
(1)With IAC valve temperature at 75°F (24)°C.
(2)With IAC valve temperature at 60°F (20)°C.
(3)With IAC valve temperature at 73°F (23)°C.