There will always be more noises from a new engine bedding in, all the oil has got to get around the engine and lube everything up which will eventually quite down. Your worrying over nothing I think :p
 
It takes about 10 mins fo driving to reach temps for the stat to open.

Dont go by the gauge as it will show 90 when in reality its probably about 75-80.

Some good pointer in gettin the coolant bled. Bentley manual also mentions raising the header tank 100mm to get a good head of pressure to remove air locks. Ive done this lately with good affect.
 
Big thanks as always phil...

Finally got my Vagcom working on my Mini Dell laptop and cleared the Codes in the engine Blocks and I did a Full scan Shortly After (hadnt started it) and this is what came up

VAG-COM Version: Release 311.2-N


Chassis Type: 1M - Seat Leon
Scan: 01,02,03,08,15,17,19,22,35,46,56

Address 01 -------------------------------------------------------
Controller: 1ML 906 032 A
Component: 1.8l R4/5VT 0001
Coding: 10510
Shop #: WSC 77875
VSSZZZ1MZ3R056288 SEZ7Z0B1737303
1 Fault Found:
17987 - Throttle Actuator (J338): Adaptation Not Started
P1579 - 35-00 - -
Readiness: 0110 0100

Address 03 -------------------------------------------------------
Controller: 8N0 907 379 G
Component: ESP FRONT MK60 0101
Coding: 0019469
Shop #: WSC 00001
Note: Excessive Comm Errors

Address 08 -------------------------------------------------------
Controller:  ö 1M0 820
Note: Excessive Comm Errors

Skipping Address 15-Airbags

Address 17 -------------------------------------------------------
Controller: 1M0 920 922 F
Component: KOMBI+WEGFAHRSP VDO V03
Coding: 05424
Shop #: WSC 00000
VSSZZZ1MZ3R056288 SEZ7Z0B1737303
2 Faults Found:
00562 - Sensor for Oil Level/Temperature (G266)
30-10 - Open or Short to B+ - Intermittent
01176 - Key
07-10 - Signal to Low - Intermittent

Address 19 -------------------------------------------------------
Controller: 6N0 909 901
Component: Gateway K<->CAN 0001
Coding: 00006
Shop #: WSC 06402
No fault code found.

Address 46 -------------------------------------------------------
Controller: 1C0 959 799 F
Component: 93 Komfortgerát HLO 0003
Coding: 00258
Shop #: WSC 06402
8 Faults Found:
01330 - Central Control Module for Central Convenience (J393)
53-10 - Supply Voltage Too Low - Intermittent
01134 - Alarm Horn (H12)
49-10 - No Communications - Intermittent
01135 - Interior Monitoring Sensors
36-10 - Open Circuit - Intermittent
01332 - Door Control Module: Passenger Side (J387)
53-10 - Supply Voltage Too Low - Intermittent
01359 - Internal Central Locking Switch: Passenger Side (E198)
27-10 - Implausible Signal - Intermittent
00929 - Locking Module for Central Locking: Front Passenger Side (F221)
27-10 - Implausible Signal - Intermittent
01333 - Door Control Module: Rear Left (J388)
53-10 - Supply Voltage Too Low - Intermittent
01334 - Door Control Module: Rear Right (J398)
53-10 - Supply Voltage Too Low - Intermittent

then once i started it after clearing the Codes on the engine block the Car felt alot better on idle and these are the ones that came back

VAG-COM Version: Release 311.2-N

Control Module Part Number: 1ML 906 032 A
Component and/or Version: 1.8l R4/5VT 0001
Software Coding: 10510
Work Shop Code: WSC 77875
Additional Info: VSSZZZ1MZ3R056288 SEZ7Z0B1737303
3 Faults Found:
17987 - Throttle Actuator (J338): Adaptation Not Started
P1579 - 35-00 - -
17695 - Boost Pressure Control Valve (N249): Open Circuit
P1287 - 35-00 - -
17748 - Camshaft Position Sensor (G40) / Engine Speed Sensor (G28): Incor. Correlation
P1340 - 35-00 - -
 
Big thanks as always phil...

Finally got my Vagcom working on my Mini Dell laptop and cleared the Codes in the engine Blocks and I did a Full scan Shortly After (hadnt started it) and this is what came up

VAG-COM Version: Release 311.2-N


Chassis Type: 1M - Seat Leon
Scan: 01,02,03,08,15,17,19,22,35,46,56

Address 01 -------------------------------------------------------
Controller: 1ML 906 032 A
Component: 1.8l R4/5VT 0001
Coding: 10510
Shop #: WSC 77875
VSSZZZ1MZ3R056288 SEZ7Z0B1737303
1 Fault Found:
17987 - Throttle Actuator (J338): Adaptation Not Started
P1579 - 35-00 - -
Readiness: 0110 0100

Address 03 -------------------------------------------------------
Controller: 8N0 907 379 G
Component: ESP FRONT MK60 0101
Coding: 0019469
Shop #: WSC 00001
Note: Excessive Comm Errors

Address 08 -------------------------------------------------------
Controller:  ö 1M0 820
Note: Excessive Comm Errors

Skipping Address 15-Airbags

Address 17 -------------------------------------------------------
Controller: 1M0 920 922 F
Component: KOMBI+WEGFAHRSP VDO V03
Coding: 05424
Shop #: WSC 00000
VSSZZZ1MZ3R056288 SEZ7Z0B1737303
2 Faults Found:
00562 - Sensor for Oil Level/Temperature (G266)
30-10 - Open or Short to B+ - Intermittent
01176 - Key
07-10 - Signal to Low - Intermittent

Address 19 -------------------------------------------------------
Controller: 6N0 909 901
Component: Gateway K<->CAN 0001
Coding: 00006
Shop #: WSC 06402
No fault code found.

Address 46 -------------------------------------------------------
Controller: 1C0 959 799 F
Component: 93 Komfortgerát HLO 0003
Coding: 00258
Shop #: WSC 06402
8 Faults Found:
01330 - Central Control Module for Central Convenience (J393)
53-10 - Supply Voltage Too Low - Intermittent
01134 - Alarm Horn (H12)
49-10 - No Communications - Intermittent
01135 - Interior Monitoring Sensors
36-10 - Open Circuit - Intermittent
01332 - Door Control Module: Passenger Side (J387)
53-10 - Supply Voltage Too Low - Intermittent
01359 - Internal Central Locking Switch: Passenger Side (E198)
27-10 - Implausible Signal - Intermittent
00929 - Locking Module for Central Locking: Front Passenger Side (F221)
27-10 - Implausible Signal - Intermittent
01333 - Door Control Module: Rear Left (J388)
53-10 - Supply Voltage Too Low - Intermittent
01334 - Door Control Module: Rear Right (J398)
53-10 - Supply Voltage Too Low - Intermittent

then once i started it after clearing the Codes on the engine block the Car felt alot better on idle and these are the ones that came back

VAG-COM Version: Release 311.2-N

Control Module Part Number: 1ML 906 032 A
Component and/or Version: 1.8l R4/5VT 0001
Software Coding: 10510
Work Shop Code: WSC 77875
Additional Info: VSSZZZ1MZ3R056288 SEZ7Z0B1737303
3 Faults Found:
17987 - Throttle Actuator (J338): Adaptation Not Started
P1579 - 35-00 - -
17695 - Boost Pressure Control Valve (N249): Open Circuit
P1287 - 35-00 - -
17748 - Camshaft Position Sensor (G40) / Engine Speed Sensor (G28): Incor. Correlation
P1340 - 35-00 - -

Check the vac hose ontop of throttle body?
 
17748/P1340/004928 - Camshaft Position Sensor (G40) / Engine Speed Sensor (G28): Incor. Correlation

Possible Causes
Timing Belt/Chain incorrectly installed
Timing Chain probably lengthened
Camshaft Position Sensor (G40) faulty
Engine Speed Sensor (G28) faulty
Possible Solutions
Check Timing Belt/Chain installation
Use Measuring Value Blocks (MVB) to Check Timing Chain
Check/Replace Camshaft Position Sensor (G40)
Check/Replace Engine Speed Sensor (G28)
Special Notes
When found in the 1.8T engine, check engine oil pressure. The oil pump pickup may be restricted.
When found in the 1.8T engine (possibly others too), check to make sure the correct G40 is installed (single gap versus 4 gap).
 
Either cam to cam timing is out or cambelt is out.

Dont bother with vag com, just check the physical marks.

Have you removed the cams? If not then your belt isnt on right. It will run no problems being out a tooth, but will feel laggy and unresponsive.

if you want pics to check things let me know as i went through this as my engine builder didnt time my cams properly when he built my engine.