A lot of people get this problem with the TransGo kits, kit is designed to enhance the stock tables without adjusting tun values, if you add kit to a tun that is already adjusted to make stock plate shift firmer it will be to firm. TransGo needs to be more specific in the shift firmness details, firm means real hard shifts in TransGo terms. Try stock table values then adjust from there.
You can shot peen the holes to make them smaller.