At relatively low tech, long range squad jumps to give you time to recover from shock and start kiting may not be an option. Something I've been considering is to treat ump assaults like siege scenarios, with dedicated assault ships that are basically siege weapons: big with tons of armor and shields to absorb the initial damage, and SLOW to save space for combat capacity. In particular, if you go with commercial engines to help with range, you can use commercial jump drives to transit the giant ships. You lose out on squadron size a bit, but the research cost for really big military jump drives is prohibitive.
As a general point, make sure to get max crew grade and full fleet training! Crew grade directly reduces jump shock duration, so invest in auxiliary commands, crew training officers, and level 5 quality for your crew pool.