Can anyone tell me what changed over the years before the 3V came out?

 

'99 had the crappy heads and EGR.

'00 up to '04 had PI heads that gave more power. No EGR.

'04 ??? More spark plug threads.

'05+ 3v.

 

are the intakes the same from 99' to 04'

 

Intakes are not the same from '99-04.

They are from '97-'99 and then '00-'04.

The shape of the intake runners on PI heads changed in '00 so a pre-'00 intake will not fit '00 and above.

 

Why are the 99' heads crappy?
Anything I should be worried about on my 99'?

 

No. They are not the "PI" (performance improved) version but other then not producing as much power they are not any worse.

 

They are prone to pop plugs as are some of the PI heads, not to mention nearly 50hp and 20ft.lbs less torque.

 

For the spark plug thread issues:

December 1996 - 4.6L 4V alignment feature added
February 1997 - 4.6L 2V head alignment feature added
September 2000 - WEP (Windsor Engine Plant) 2V head alignment feature modified (4.6/5.4/6.8)
November 2002 - WEP introduced long thread heads on 2V (all)
May 2003 - REP (Romeo Engine Plant) introduced long-thread heads on 4V 4.6 and 5.4
November 2003 - REP introduced long-thread heads on 2V and modified alignment feature

In 1999, and 2001, an interim fix was done for a cross-threading issue.
Original process:

Step 1 - Zero torque spark plug (air tool)
Step 2 - Torque to 16-20Nm final torque (DC Run down), monitor at 6-12Nm, and final torque must be reached within 0-360 degrees.

New process (addressed the possibility of applying installation torque for more than 25 degrees of rotation)
Step 1 - Zero torque spark plug (air tool)
Step 2 - Torque to 16-20Nm final torque (DC Run down) start monitor at 6-12Nm, and final torque must be reached within 3-25 degrees.

Another action to address cross-threading was the addition of an alignment feature to lead the plug into the hole.