<VV> PG questions

[Kinzelman, Andy]

Guys,
I had differential issues with my 63 Monza, so I swapped a long disused PG transaxle into it two weekends back.
I used the existing TC - as the 'new' transaxle had none.  I also gave it a new modulator, but I did not mess with the low band adjustment.  The fluid left in the trans looked good - I just topped it up; it is not low.  The bottom of the pan is moderately dented; I plan to change it relatively soon.
Sometimes the trans shifts like a champ - but sometimes it surges badly when upshifting (often worse when cold; but not exclusively).  Also, sometimes if I let it idle in neutral it won't go into gear right away when I shift into drive.
I have been working on the theory that it has to flush some old 'gunk' out; and that when I change the pan , filter, & oil it will be happier.  Is this realistic; or should I be looking at something else?
Thanks,
Andy K.