Something is not quite right
Straut - that hard shift 1-2 is not normal. When I corrected my reassembly error my shifting went back to smooth as glass. In fact I can't tell when the car shifts after it warms up. I bet you have a gremlin that can be fixed. After I fixed the problem I was confused - how would an air intake leak cause a tranny problem? So I loosened the air intake and drove around the block - the problem came back.
I think that with less turbo back pressure the engine spools up too much between shifts and makes it jerky. When the leak is fixed the engine takes long to rev up and that matches the transmission setup better.
BTW I didn't notice any loss of power.
1983 300D Turbo
1995 E320 Wagon
2001 MR2 Spyder
2001 Subura WRX Sedan