lacks power only when cold, poor mpg, verify timing Options

[VavAlephVav]

So I've only had the car a little while and this is the first time I've been driving it when its Butt cold outside. 5*F/-15*C
when the motor is cold it hesitates more than I've ever seen it and downright seems to have no power up through 3000 rpm or so.
of course this motor warms up fast so it only does it the first couple of times I shift and then it goes away, except that my gas mileage is down to like 22mpg or so.(although I was only getting 26 or so before)
OK, so I understand that all motors act funny when its cold, but this one seems worse than it should be.
I did just replace the water pump... and I know I turned the crank with a wrench after installing the belt and checked the marks, but I am paranoid that somehow when I
adjusted the tensioner it got off by one tooth or something. sadly you have to do the biggest part of the job to get the motor bracket off so that you could get the top timing cover off just to verify the mark and see if its timed right or not.
I'm tempted to drill a small hole in the timing cover so that I could see the cam mark and verify it before I spend the whole day taking the motor apart and maybe find out that the timing is ok.

I'm wondering If you check the ignition timing with a timing light will that verify the valve timing by the timing belt or no?
also I need a whole bunch of tune up stuff, so far I have new cheap copper plugs but I still need stuff like wires, cap/rotor, fuel filter, IAC, and probably an EGR even though I have not tested it. and my air intake hose is held together by ducktape
and is there a certain period of time the computer needs to relearn after its been unplugged a while? I've only gone through one tank of gass since I did the water pump.

any insight you guys have as to how to check and be sure before I tear the whole thing apart would be appreciated,

[VavAlephVav]

its a 5 speed, new fluid cause I just changed the cv, wheel bearing, ball joint ect. 80-90w Castrol.
its a 1994 st204 with the 5s-fe, but it has had the motor replaced with a 5s-fe from a camry - not sure what year but the motor is at about 140k miles.
ya, I still need fuel filter, cap, wires, ect I think I'll take off the egr and clean it if it ever gets back above -20000* around here
there are no warning lights on 'cept the airbag light
I have not tried to use the jumper and retrieve any stored engine codes though

I was listening to other peoples tell me that the only difference between copper and platinum was how long they last before you have to change them and
so I was putting that theory to the test, since these are really easy to change.
I'll go get some decent plugs soon