My tranny problems were bearings, never had any serious trouble shifting, but it made me swear off Japanese.Sounds like your current troubles, if internal to the tranny, would be synchros going bad, little things that help align the gears so it shifts smoother. If they were going bad, you might be able to try double clutching, that's what people had to do before they invented synchros. Another possibility is that the shifter linkages are gunked up. The shifter inside the car is connected to the tranny with two cables, and there are bushings where these cables attach to the shift mechanisms on the tranny. At one point, mine were really full of salt and road grime, when I took them off, cleaned and lubricated them, seemed like shifting was a lot smoother. Maybe yours are high friction, causing the tranny to not be able to shift fully to the position where it would drop into gear.
http://forums.genvibe.com/zerofile/6856/5speed.jpg shows these at the tranny end.I have had occiasional problems, even when brand new, shifting into reverse, or first froma a dead stop, and when it happens I usually shift to neutral, let the clutch out, put the clutch in, and try to shift back into gear. Seems to spin something internal to let it shift ok. I think that's just the nature of these trannies, not something that indicates a reliability problem or a failure.having a second tranny go in a short period of time is quite frustrating. These things should be bullet proof, especially if you listen to all the hype about Toyota reliability. If they really did put in a new tranny, and they warranteed it and your still in that warranty, then it seems like they should pay more than 20%. THey don't warranty clutches, because there's no way to prove that it wasn't the driver casuing the clutch to burn up. I'd say first try the easy and low cost option, clean and lube those bushings