Yeah, that's a pain I'd rather avoid, but it's doable with connection time if the first leg holds up.
(The current plan has me overnighting in SFO on the way back, so that part doesn't matter).


Here's an alternative (breaking most of the rules I laid out above )

OUTBOUND:
Monday 26th April
CO106
IAH - EWR dep 10:45a.m. arr 3.25pm

CO702
EWR - SFO dep 4:45 p.m. arr 8:07 p.m.

Change Planes. Connect time in San Francisco, CA (SFO) is 2 hours 18 minutes .

CO7550 (United metal)
SFO - GEG dep 10:25 p.m. arr 12:28 a.m. +1 Day


RETURN
Wednesday 28 April

CO 7603 (United metal)
GEG - SFO dep 6:25 p.m. arr 8.29 p.m. (United metal)

Change Planes. Connect time in San Francisco, CA (SFO) is 1 hour 51 minutes .

CO1829
SFO - EWR dep: 10:20 p.m. arr 6:37 a.m. +1 Day

connect time in EWR is 1hr18mins

CO211
EWR - IAH dep 7.55 a.m. arr 10:33 a.m.


That comes in around 935USD, and 9424 miles.


Flying EWR - SAN - IAH puts me over my 1000USD, but there may be some other options in there.

Flying IAH - EWR on the outbound is also a bit dodgy, because of the chance of disconnects. (However in my experience that route is fairly stable, it's getting stuck in SFO due to fog or somesuch that is the issue. If I miss the evening flight from SFO, there is a morning flight I can take ).