2001 Avalon TB replace issues.

[apache2223]

I'm replacing the TB on my neighbor's 2001 Avalon 3.0(Also did the spark plugs, valve cover gaskets, replaced several vacuum lines, water pump, crank and cam seals, tensioner, idler pulley and drained and replaced antifreeze with Toyota red). Got it all back together and it fired right up and idled perfectly, long enough to get the engine up to temp and top off the antifreeze. Then I did a vacuum test, just because I have no life and it's the kinda thing I do for fun...lol. I have a fairly new Snap-On Vacuum Gauge that I've used on several cars and the readings have always been consistently between 15-20 in.HG. This car was idling about 750 RPM and was reading a very steady 12 on the gauge. Did the test where you rev it up real quick or snap the throttle and it reacted correctly(went down to around 5 in.HG, then up to 20+, then back to around 12). Then it started missing a bit. Not popping, but almost. Like a very faint popping I guess. Now rewind back to my install of the belt. The belt he got was ........different. It had arrows going the direction of "forward" and the 3 marks were even with the cogs, so it was impossible to line them up exact. I had to either be 1/2 tooth to the right or the left of the mark on the belt. Also, the mark for the crank position wore off unexplicably. The 2 marks for the camshaft gears are on there good however. So I used the old belt and the marks I made before removing it, to get the 3rd mark back. I installed it RH gear first, then placed an alligator clip, then LH gear, clip, then down to the crank, but this is where I had issues. The mark is at about the 4 0'clock area on the crank gear, but the belt was about 2 teeth to the left or counter-clockwise of the crank gear mark. It was this way even before the mark disappeared, so I marked it correctly. Also, I hadn't installed the tensioner yet. So I watched what seemed to be my 1,000th video and saw where a guy said he gets all the marks lined up using the belt in no particular way and then takes the belt off the crank gear and moves the 2 cam gears clockwise 1 tooth(so they both move equally 1 tooth), which enabled him to be right on at the crank gear. Using this logic, I moved the 2 gears clockwise just enough to be able to get the crank gear and belt mark to match(about 1 1/2 teeth clockwise with the 2 cam gears). Installed tensioner, pulled the pin, rotated engine 2x and with the crank gear back to TDC, the 2 cam gears were still about 1 1/2 teeth clock wise past the correct mark.......which is kinda what I thought would happen....lol. But I put everything back together enough to start it and it started right up and ran fine, then I shut it off, replaced everything and then is when I ran the vacuum tests. I guess my question is, when I disassemble this thing again, to get the belt right, how in the heck do I get these marks to line up?.....lol. I'm guessing the low vacuum reading is because I retarded the timing? And has anyone ever seen a TB with the marks even with the cogs on the belt? Any help whatsoever would be greatly appreciated. I still have all the brakes and struts to do, so I'd really like to get this belt issue fixed. Thanks in advance!