I'm upgrading 3rd and 4th gears; synchros; and shift sleeve of a 1999 C60 gearbox to 2003 parts. I've noticed that the upgraded sleeve slides pass the locking teeth and over 3rd gear. Where as the sleeve from the 1999 box stop sliding after the locking teeth. Is this normal?

Just depends on circumference of gear teeth. Some are smaller and so sliding collar will pass right on over.
No big deal.

4th gear is slightly larger than 3rd gear and the sleeve hits the teeth. So your saying that this maybe a problem?

No. I'm saying it's no problem. 
It's perfectly normal design. In operation the sliding collar is prevented from moving too far by the shift fork which is attached to the shift shaft which is indexed by it's three detents and usually has two final limit stops.

The C60 difficult shift /grauch countermeasure has a parts list. Its not exactly what you asked for, but it might give you a double check on all the matched parts.
 
TSB_2001_6spd_GTS_Gear_difficulty.pdf
 

The only parts of this TSB that may apply to fitting a C60 to a ZZW30 are the No.1 gear shift fork shaft, No.1 gear shift head, and No.3 gear shift fork shaft. The No.3 gear shift fork shaft in the ZZW30 C65 is the updated part. So this make sense. However, the No.1 gear shift fork shaft is a different part number and the No.1 gear shift head is the 99-01 C60 part in the ZZW30 C65. ???
 
BTW: Where did you find this TSB. I'm asking this because, I've been looking for the TSB for the 3rd and 4th synchro upgrade and cannot find it. I got the part no. off the Monkey Wrench Racing Web Site.

Just had an interest as my C52 is getting tired and I was looking at upgrade paths. I found that one aug of last year but have forgotten where. Im not in the Toyota supplier chain anymore so it was just a web based search. Did you find a source for the equivalent of the Toyota special tools? Most people don't realise they pull on circlip grooves or the fork interface rather than screwing into the gear or prying on the backface. They are hard to find short of fabricating them on the spot. 

With the exception of a Toyota puller set (which I found cheep on Gumtree) and a fitting tool (which was only something like $30 new from a Toyota dealership) I've had to fabricate many of the tools needed to over haul the box.