when upgrading my ship some of the upgrades have not installed eg.... 4 energy points
2 attack points
and some ship decks

apart from that great game best on facebook.....love playing.......keep up the good work

you mean stats you got from rank points are disapearing? IDK if thats the case. Also, some advice, do not put rank points into crew, deck is much more valuable then crew in the long run.

Engineers are quite valuable.

Cores, cores, cores are what matter. If I put 17 rp's in engineers I would have 34 energy, if I put 17 in decks, I would have a graviton core mk IV which gives me 35 energy, but thats only the secind teir, every teir increases in efficiency, Im almost up to quantum capacitors.

Your ship can have a maximum of 3 cores and 4 relays, so max them out. There's no limit on engineers and they stack with cores.

Yes, but as you go through the research trees, the reactors get bigger, and bigger, and bigger. You will need to put the majority of RP's into decks if you want to put even one of each high level module.

Easy solution - don't put one of each module on your ship. Decide what's most important for your play style and focus on that. If you're having trouble fitting max cores and relays on your ship, but they're important to you, then you need to rethink your modules.