If you throw the cam gears on, you should be able to see the vertical line on the timing cover backing plate through the small hole drilled into the gear itself at TDC.
It definitely sounds like a timing issue, however hard to say if it is a mechanical or triggering issue. I have seen cam and crank triggers mixed up previously causing a similar fault to what you are describing(backfire into intake).
I have a heap of information at home on the 3S-GE, however the earliest I can get to that is Tuesday next week.