Chris, did you remove the lower spring plates and swap them side for side, inverting them as you did? Most shock conversions call for this to gain the extra distance for proper operation. The ears where the shock links attached should now point down instead of up as originally installed.
I installed a tube shock conversion on my Midget years ago, but since that time I've heard so many reports of bottoming such as you're experiencing and other problems I'm now leaning in favor of a good set of rebuilt or new lever action shocks instead of a tube conversion. I'd change mine back except for the panhard rod bracket I incorporated into the shock mount which I don't want to redo. My MGA will definitely stay with lever action shocks.
'73 Midget (V6)
'59 MGA (I6) under construction
'73 Lotus Europa
"There is a fine line between a hobby and mental illness"