I got a scion tc 2006 manual transmision and im having
this issue, sometimes y takes long to start up(Like 3 or 4 sec) and others start normaly, What can be?

 

You gave us way too much information. Give us a while to comprehend it all.

 

okay np

 

i was thinking could it be fuel pump problem or something? it got 44K miles and the engine had power idk what get into it xd maybe some relay problem? btw it make like some relay noise wend i feel it's taking longer to start the engine. I stop the inicion and you hear like some relay noise then i give it another try and start normally

 

Check your battery if the weather is cold would lag to turn on

 

im from puerto rico it's a tropical weather most time hot and the battery is new it had 2 week of use

 

Try cleaning your throttle body. Did this start to happen when you changed the battery? Does it only do it when cold? Does the battery have enough cold cranking amps to start up the car? A lower amp would still start the car but it would take longer.

 

no, the problem persists before and after i changed the battery. I gonna check cleaning the throttle body

 

Try that and check your cables and terminals

 

Might you have another transponder key on your keyring interfering with the Scion transponder ECU?

 

the alarm dosnt work so it removed also the key control pad

 

Not all diagnostic codes illuminate the check engine light. If you have access to a meter, you could see if something's throwing a code.