Problem:
I have a 2000 safari with 115K miles. A few of months ago I noticed a jerk (hesitation) while driving. I would have the cruse on and the van would jerk sporadically, it did not constantly do it. Now it also sporadically does it when I accelerate. I feel it does it more when it is cold out, I have not determined if it happen more when there is less fuel in the tank. I have narrowed it down to engine; I can still feel/hear the hesitation when the van is in park.
The other problem I have is with acceleration. The engine revs up but the van does not move as fast as I feel it should be, then after 30 to 45 second it catches up. It feels like the trany is in two gears at the same time or the torch converter is not completely engaged. If I let up on the gas it catches up sooner. I hope this makes sense.

What I have done:
Recently I have replaced the coil, spark plugs and spark plug wires. Around 75k I had the injector cleaned and the trany flushed. I did replace the fuel filter 1 or 2 years ago.

You might want to check the distributor cap. The cap on your engine uses cross-over bussing, and insulation breakdown in the cap can create the misfire you describe. Aftermarket caps seem to last only a fraction of the OEM parts. The plugs, wires, and coil probably don't matter as much, but the aftermarket has evidently not figured out the insulation yet.

As for the apparent slipping, there are lots of possibilities, but the torque converter isn't as likely as some others. Slipping in the torque converter clutch might create some shudder while at cruise, but shouldn't be causing a problem during acceleration. If the trans is actually slipping, check the line pressure (fitting on the left side of the trans) in various ranges. Low pressure can cause poor clutch engagement, particularly in the 3-4 clutch and direct clutch, allowing slippage. Scanning the PCM for transmission trouble codes can also reveal some information.

Fix the misfire problem first. Misfire's may feel like and/or create transmission problems.